diff --git a/config.go b/config.go
index 21b49572..a31e498e 100644
--- a/config.go
+++ b/config.go
@@ -3,7 +3,6 @@ package wazero
 import (
 	"context"
 	"errors"
-	"fmt"
 	"io"
 	"io/fs"
 	"math"
@@ -11,6 +10,7 @@ import (
 	"github.com/tetratelabs/wazero/api"
 	"github.com/tetratelabs/wazero/internal/engine/compiler"
 	"github.com/tetratelabs/wazero/internal/engine/interpreter"
+	fs2 "github.com/tetratelabs/wazero/internal/fs"
 	"github.com/tetratelabs/wazero/internal/wasm"
 )
 
@@ -452,21 +452,15 @@ type moduleConfig struct {
 	// environKeys allow overwriting of existing values.
 	environKeys map[string]int
 
-	// preopenFD has the next FD number to use
-	preopenFD uint32
-	// preopens are keyed on file descriptor and only include the Path and FS fields.
-	preopens map[uint32]*wasm.FileEntry
-	// preopenPaths allow overwriting of existing paths.
-	preopenPaths map[string]uint32
+	fs *fs2.FSConfig
 }
 
 func NewModuleConfig() ModuleConfig {
 	return &moduleConfig{
 		startFunctions: []string{"_start"},
 		environKeys:    map[string]int{},
-		preopenFD:      uint32(3), // after stdin/stdout/stderr
-		preopens:       map[uint32]*wasm.FileEntry{},
-		preopenPaths:   map[string]uint32{},
+
+		fs: fs2.NewFSConfig(),
 	}
 }
 
@@ -493,7 +487,7 @@ func (c *moduleConfig) WithEnv(key, value string) ModuleConfig {
 // WithFS implements ModuleConfig.WithFS
 func (c *moduleConfig) WithFS(fs fs.FS) ModuleConfig {
 	ret := *c // copy
-	ret.setFS("/", fs)
+	ret.fs = ret.fs.WithFS(fs)
 	return &ret
 }
 
@@ -542,23 +536,10 @@ func (c *moduleConfig) WithRandSource(source io.Reader) ModuleConfig {
 // WithWorkDirFS implements ModuleConfig.WithWorkDirFS
 func (c *moduleConfig) WithWorkDirFS(fs fs.FS) ModuleConfig {
 	ret := *c // copy
-	ret.setFS(".", fs)
+	ret.fs = ret.fs.WithWorkDirFS(fs)
 	return &ret
 }
 
-// setFS maps a path to a file-system. This is only used for base paths: "/" and ".".
-func (c *moduleConfig) setFS(path string, fs fs.FS) {
-	// Check to see if this key already exists and update it.
-	entry := &wasm.FileEntry{Path: path, FS: fs}
-	if fd, ok := c.preopenPaths[path]; ok {
-		c.preopens[fd] = entry
-	} else {
-		c.preopens[c.preopenFD] = entry
-		c.preopenPaths[path] = c.preopenFD
-		c.preopenFD++
-	}
-}
-
 // toSysContext creates a baseline wasm.SysContext configured by ModuleConfig.
 func (c *moduleConfig) toSysContext() (sys *wasm.SysContext, err error) {
 	var environ []string // Intentionally doesn't pre-allocate to reduce logic to default to nil.
@@ -578,24 +559,9 @@ func (c *moduleConfig) toSysContext() (sys *wasm.SysContext, err error) {
 		environ = append(environ, key+"="+value)
 	}
 
-	// Ensure no-one set a nil FD. We do this here instead of at the call site to allow chaining as nil is unexpected.
-	rootFD := uint32(0) // zero is invalid
-	setWorkDirFS := false
-	preopens := c.preopens
-	for fd, entry := range preopens {
-		if entry.FS == nil {
-			err = fmt.Errorf("FS for %s is nil", entry.Path)
-			return
-		} else if entry.Path == "/" {
-			rootFD = fd
-		} else if entry.Path == "." {
-			setWorkDirFS = true
-		}
-	}
-
-	// Default the working directory to the root FS if it exists.
-	if rootFD != 0 && !setWorkDirFS {
-		preopens[c.preopenFD] = &wasm.FileEntry{Path: ".", FS: preopens[rootFD].FS}
+	preopens, err := c.fs.Preopens()
+	if err != nil {
+		return nil, err
 	}
 
 	return wasm.NewSysContext(math.MaxUint32, c.args, environ, c.stdin, c.stdout, c.stderr, c.randSource, preopens)
diff --git a/config_test.go b/config_test.go
index 7a0c9bcf..8d4600b6 100644
--- a/config_test.go
+++ b/config_test.go
@@ -9,6 +9,7 @@ import (
 	"testing/fstest"
 
 	"github.com/tetratelabs/wazero/api"
+	"github.com/tetratelabs/wazero/internal/fs"
 	"github.com/tetratelabs/wazero/internal/testing/require"
 	"github.com/tetratelabs/wazero/internal/wasm"
 )
@@ -438,7 +439,7 @@ func TestModuleConfig_toSysContext(t *testing.T) {
 				nil,            // stdout
 				nil,            // stderr
 				nil,            // randSource
-				map[uint32]*wasm.FileEntry{ // openedFiles
+				map[uint32]*fs.FileEntry{ // openedFiles
 					3: {Path: "/", FS: testFS},
 					4: {Path: ".", FS: testFS},
 				},
@@ -455,7 +456,7 @@ func TestModuleConfig_toSysContext(t *testing.T) {
 				nil,            // stdout
 				nil,            // stderr
 				nil,            // randSource
-				map[uint32]*wasm.FileEntry{ // openedFiles
+				map[uint32]*fs.FileEntry{ // openedFiles
 					3: {Path: "/", FS: testFS2},
 					4: {Path: ".", FS: testFS2},
 				},
@@ -472,7 +473,7 @@ func TestModuleConfig_toSysContext(t *testing.T) {
 				nil,            // stdout
 				nil,            // stderr
 				nil,            // randSource
-				map[uint32]*wasm.FileEntry{ // openedFiles
+				map[uint32]*fs.FileEntry{ // openedFiles
 					3: {Path: ".", FS: testFS},
 				},
 			),
@@ -488,7 +489,7 @@ func TestModuleConfig_toSysContext(t *testing.T) {
 				nil,            // stdout
 				nil,            // stderr
 				nil,            // randSource
-				map[uint32]*wasm.FileEntry{ // openedFiles
+				map[uint32]*fs.FileEntry{ // openedFiles
 					3: {Path: "/", FS: testFS},
 					4: {Path: ".", FS: testFS2},
 				},
@@ -505,7 +506,7 @@ func TestModuleConfig_toSysContext(t *testing.T) {
 				nil,            // stdout
 				nil,            // stderr
 				nil,            // randSource
-				map[uint32]*wasm.FileEntry{ // openedFiles
+				map[uint32]*fs.FileEntry{ // openedFiles
 					3: {Path: ".", FS: testFS},
 					4: {Path: "/", FS: testFS2},
 				},
@@ -576,7 +577,7 @@ func TestModuleConfig_toSysContext_Errors(t *testing.T) {
 }
 
 // requireSysContext ensures wasm.NewSysContext doesn't return an error, which makes it usable in test matrices.
-func requireSysContext(t *testing.T, max uint32, args, environ []string, stdin io.Reader, stdout, stderr io.Writer, randsource io.Reader, openedFiles map[uint32]*wasm.FileEntry) *wasm.SysContext {
+func requireSysContext(t *testing.T, max uint32, args, environ []string, stdin io.Reader, stdout, stderr io.Writer, randsource io.Reader, openedFiles map[uint32]*fs.FileEntry) *wasm.SysContext {
 	sys, err := wasm.NewSysContext(max, args, environ, stdin, stdout, stderr, randsource, openedFiles)
 	require.NoError(t, err)
 	return sys
diff --git a/examples/wasi/testdata/sub/test.txt b/examples/wasi/testdata/sub/test.txt
new file mode 100644
index 00000000..4b45af5e
--- /dev/null
+++ b/examples/wasi/testdata/sub/test.txt
@@ -0,0 +1 @@
+greet sub dir
diff --git a/experimental/fs.go b/experimental/fs.go
new file mode 100644
index 00000000..b00bd3ee
--- /dev/null
+++ b/experimental/fs.go
@@ -0,0 +1,21 @@
+package experimental
+
+import (
+	"context"
+	"io/fs"
+
+	"github.com/tetratelabs/wazero/api"
+	internalfs "github.com/tetratelabs/wazero/internal/fs"
+)
+
+// WithFS overrides fs.FS in the context-based manner. Caller needs to take responsibility for closing the filesystem.
+func WithFS(ctx context.Context, fs fs.FS) (context.Context, api.Closer, error) {
+	fsConfig := internalfs.NewFSConfig().WithFS(fs)
+	preopens, err := fsConfig.Preopens()
+	if err != nil {
+		return nil, nil, err
+	}
+
+	fsCtx := internalfs.NewContext(preopens)
+	return context.WithValue(ctx, internalfs.Key{}, fsCtx), fsCtx, nil
+}
diff --git a/experimental/fs_test.go b/experimental/fs_test.go
new file mode 100644
index 00000000..abdef6ae
--- /dev/null
+++ b/experimental/fs_test.go
@@ -0,0 +1,41 @@
+package experimental_test
+
+import (
+	"context"
+	_ "embed"
+	"log"
+	"testing"
+	"testing/fstest"
+
+	"github.com/tetratelabs/wazero/experimental"
+	"github.com/tetratelabs/wazero/internal/fs"
+	"github.com/tetratelabs/wazero/internal/testing/require"
+)
+
+// This is a very basic integration of fs config. The main goal is to show how it is configured.
+func TestWithFS(t *testing.T) {
+	fileName := "animals.txt"
+	mapfs := fstest.MapFS{fileName: &fstest.MapFile{Data: []byte(`animals`)}}
+
+	// Set context to one that has experimental fs config
+	ctx, closer, err := experimental.WithFS(context.Background(), mapfs)
+	if err != nil {
+		log.Panicln(err)
+	}
+	defer closer.Close(ctx)
+
+	v := ctx.Value(fs.Key{})
+	require.NotNil(t, v)
+	fsCtx, ok := v.(*fs.Context)
+	require.True(t, ok)
+
+	entry, ok := fsCtx.OpenedFile(3)
+	require.True(t, ok)
+	require.Equal(t, "/", entry.Path)
+	require.Equal(t, mapfs, entry.FS)
+
+	entry, ok = fsCtx.OpenedFile(4)
+	require.True(t, ok)
+	require.Equal(t, ".", entry.Path)
+	require.Equal(t, mapfs, entry.FS)
+}
diff --git a/internal/fs/fs.go b/internal/fs/fs.go
new file mode 100644
index 00000000..fb25de87
--- /dev/null
+++ b/internal/fs/fs.go
@@ -0,0 +1,172 @@
+package fs
+
+import (
+	"context"
+	"fmt"
+	"io/fs"
+	"math"
+	"sync/atomic"
+)
+
+// Key is a context.Context Value key. It allows overriding fs.FS for WASI.
+//
+// See https://github.com/tetratelabs/wazero/issues/491
+type Key struct{}
+
+// FileEntry maps a path to an open file in a file system.
+//
+// Note: This does not introduce cycles because the types here are in the package "wasi" not "internalwasi".
+type FileEntry struct {
+	Path string
+	FS   fs.FS
+	// File when nil this is a mount like "." or "/".
+	File fs.File
+}
+
+type Context struct {
+	// openedFiles is a map of file descriptor numbers (>=3) to open files (or directories) and defaults to empty.
+	// TODO: This is unguarded, so not goroutine-safe!
+	openedFiles map[uint32]*FileEntry
+
+	// lastFD is not meant to be read directly. Rather by nextFD.
+	lastFD uint32
+}
+
+func NewContext(openedFiles map[uint32]*FileEntry) *Context {
+	var fsCtx Context
+	if openedFiles == nil {
+		fsCtx.openedFiles = map[uint32]*FileEntry{}
+		fsCtx.lastFD = 2 // STDERR
+	} else {
+		fsCtx.openedFiles = openedFiles
+		fsCtx.lastFD = 2 // STDERR
+		for fd := range openedFiles {
+			if fd > fsCtx.lastFD {
+				fsCtx.lastFD = fd
+			}
+		}
+	}
+	return &fsCtx
+}
+
+// nextFD gets the next file descriptor number in a goroutine safe way (monotonically) or zero if we ran out.
+// TODO: opendFiles is still not goroutine safe!
+// TODO: This can return zero if we ran out of file descriptors. A future change can optimize by re-using an FD pool.
+func (c *Context) nextFD() uint32 {
+	if c.lastFD == math.MaxUint32 {
+		return 0
+	}
+	return atomic.AddUint32(&c.lastFD, 1)
+}
+
+// Close implements io.Closer
+func (c *Context) Close(_ context.Context) (err error) {
+	// Close any files opened in this context
+	for fd, entry := range c.openedFiles {
+		delete(c.openedFiles, fd)
+		if entry.File != nil { // File is nil for a mount like "." or "/"
+			if e := entry.File.Close(); e != nil {
+				err = e // This means the err returned == the last non-nil error.
+			}
+		}
+	}
+	return
+}
+
+// CloseFile returns true if a file was opened and closed without error, or false if not.
+func (c *Context) CloseFile(fd uint32) (bool, error) {
+	f, ok := c.openedFiles[fd]
+	if !ok {
+		return false, nil
+	}
+	delete(c.openedFiles, fd)
+
+	if f.File == nil { // TODO: currently, this means it is a pre-opened filesystem, but this may change later.
+		return true, nil
+	}
+	if err := f.File.Close(); err != nil {
+		return false, err
+	}
+	return true, nil
+}
+
+// OpenedFile returns a file and true if it was opened or nil and false, if not.
+func (c *Context) OpenedFile(fd uint32) (*FileEntry, bool) {
+	f, ok := c.openedFiles[fd]
+	return f, ok
+}
+
+// OpenFile returns the file descriptor of the new file or false if we ran out of file descriptors
+func (c *Context) OpenFile(f *FileEntry) (uint32, bool) {
+	newFD := c.nextFD()
+	if newFD == 0 {
+		return 0, false
+	}
+	c.openedFiles[newFD] = f
+	return newFD, true
+}
+
+type FSConfig struct {
+	// preopenFD has the next FD number to use
+	preopenFD uint32
+	// preopens are keyed on file descriptor and only include the Path and FS fields.
+	preopens map[uint32]*FileEntry
+	// preopenPaths allow overwriting of existing paths.
+	preopenPaths map[string]uint32
+}
+
+func NewFSConfig() *FSConfig {
+	return &FSConfig{
+		preopenFD:    uint32(3), // after stdin/stdout/stderr
+		preopens:     map[uint32]*FileEntry{},
+		preopenPaths: map[string]uint32{},
+	}
+}
+
+// setFS maps a path to a file-system. This is only used for base paths: "/" and ".".
+func (c *FSConfig) setFS(path string, fs fs.FS) {
+	// Check to see if this key already exists and update it.
+	entry := &FileEntry{Path: path, FS: fs}
+	if fd, ok := c.preopenPaths[path]; ok {
+		c.preopens[fd] = entry
+	} else {
+		c.preopens[c.preopenFD] = entry
+		c.preopenPaths[path] = c.preopenFD
+		c.preopenFD++
+	}
+}
+
+func (c *FSConfig) WithFS(fs fs.FS) *FSConfig {
+	ret := *c // copy
+	ret.setFS("/", fs)
+	return &ret
+}
+
+func (c *FSConfig) WithWorkDirFS(fs fs.FS) *FSConfig {
+	ret := *c // copy
+	ret.setFS(".", fs)
+	return &ret
+}
+
+func (c *FSConfig) Preopens() (map[uint32]*FileEntry, error) {
+	// Ensure no-one set a nil FD. We do this here instead of at the call site to allow chaining as nil is unexpected.
+	rootFD := uint32(0) // zero is invalid
+	setWorkDirFS := false
+	preopens := c.preopens
+	for fd, entry := range preopens {
+		if entry.FS == nil {
+			return nil, fmt.Errorf("FS for %s is nil", entry.Path)
+		} else if entry.Path == "/" {
+			rootFD = fd
+		} else if entry.Path == "." {
+			setWorkDirFS = true
+		}
+	}
+
+	// Default the working directory to the root FS if it exists.
+	if rootFD != 0 && !setWorkDirFS {
+		preopens[c.preopenFD] = &FileEntry{Path: ".", FS: preopens[rootFD].FS}
+	}
+
+	return preopens, nil
+}
diff --git a/internal/fs/fs_test.go b/internal/fs/fs_test.go
new file mode 100644
index 00000000..4f367dd4
--- /dev/null
+++ b/internal/fs/fs_test.go
@@ -0,0 +1,49 @@
+package fs
+
+import (
+	"context"
+	"io/fs"
+	"os"
+	"path"
+	"testing"
+
+	"github.com/tetratelabs/wazero/internal/testing/require"
+)
+
+// testCtx is an arbitrary, non-default context. Non-nil also prevents linter errors.
+var testCtx = context.WithValue(context.Background(), struct{}{}, "arbitrary")
+
+func TestContext_Close(t *testing.T) {
+	tempDir := t.TempDir()
+	pathName := "test"
+	file, _ := createWriteableFile(t, tempDir, pathName, make([]byte, 0))
+
+	fsc := NewContext(map[uint32]*FileEntry{
+		3: {Path: "."},
+		4: {Path: path.Join(".", pathName), File: file},
+	})
+
+	// Verify base case
+	require.True(t, len(fsc.openedFiles) > 0, "fsc.openedFiles was empty")
+
+	// Closing should not err.
+	require.NoError(t, fsc.Close(testCtx))
+
+	// Verify our intended side-effect
+	require.Equal(t, 0, len(fsc.openedFiles), "expected no opened files")
+
+	// Verify no error closing again.
+	require.NoError(t, fsc.Close(testCtx))
+}
+
+// createWriteableFile uses real files when io.Writer tests are needed.
+func createWriteableFile(t *testing.T, tmpDir string, pathName string, data []byte) (fs.File, fs.FS) {
+	require.NotNil(t, data)
+	absolutePath := path.Join(tmpDir, pathName)
+	require.NoError(t, os.WriteFile(absolutePath, data, 0o600))
+
+	// open the file for writing in a custom way until #390
+	f, err := os.OpenFile(absolutePath, os.O_RDWR, 0o600)
+	require.NoError(t, err)
+	return f, os.DirFS(tmpDir)
+}
diff --git a/internal/wasm/call_context.go b/internal/wasm/call_context.go
index 6bce5917..32cae816 100644
--- a/internal/wasm/call_context.go
+++ b/internal/wasm/call_context.go
@@ -90,7 +90,7 @@ func (m *CallContext) CloseWithExitCode(ctx context.Context, exitCode uint32) (e
 
 // close marks this CallContext as closed and releases underlying system resources without removing
 // from the store.
-func (m *CallContext) close(_ context.Context, exitCode uint32) (c bool, err error) {
+func (m *CallContext) close(ctx context.Context, exitCode uint32) (c bool, err error) {
 	// Note: If you use the context.Context param, don't forget to coerce nil to context.Background()!
 
 	closed := uint64(1) + uint64(exitCode)<<32 // Store exitCode as high-order bits.
@@ -98,7 +98,7 @@ func (m *CallContext) close(_ context.Context, exitCode uint32) (c bool, err err
 		return false, nil
 	}
 	if sys := m.Sys; sys != nil { // ex nil if from ModuleBuilder
-		return true, sys.Close()
+		return true, sys.FS().Close(ctx)
 	}
 	return true, nil
 }
diff --git a/internal/wasm/call_context_test.go b/internal/wasm/call_context_test.go
index 055453a9..71305924 100644
--- a/internal/wasm/call_context_test.go
+++ b/internal/wasm/call_context_test.go
@@ -3,9 +3,9 @@ package wasm
 import (
 	"context"
 	"fmt"
-	"path"
 	"testing"
 
+	"github.com/tetratelabs/wazero/internal/fs"
 	"github.com/tetratelabs/wazero/internal/testing/require"
 )
 
@@ -141,10 +141,6 @@ func TestCallContext_Close(t *testing.T) {
 	}
 
 	t.Run("calls SysContext.Close()", func(t *testing.T) {
-		tempDir := t.TempDir()
-		pathName := "test"
-		file, _ := createWriteableFile(t, tempDir, pathName, make([]byte, 0))
-
 		sys, err := NewSysContext(
 			0,   // max
 			nil, // args
@@ -153,26 +149,29 @@ func TestCallContext_Close(t *testing.T) {
 			nil, // stdout
 			nil, // stderr
 			nil, // randSource
-			map[uint32]*FileEntry{ // openedFiles
+			map[uint32]*fs.FileEntry{ // openedFiles
 				3: {Path: "."},
-				4: {Path: path.Join(".", pathName), File: file},
 			},
 		)
 		require.NoError(t, err)
 
+		fsCtx := sys.FS()
+
 		moduleName := t.Name()
 		m, err := s.Instantiate(context.Background(), &Module{}, moduleName, sys, nil)
 		require.NoError(t, err)
 
 		// We use side effects to determine if Close in fact called SysContext.Close (without repeating sys_test.go).
 		// One side effect of SysContext.Close is that it clears the openedFiles map. Verify our base case.
-		require.True(t, len(sys.openedFiles) > 0, "sys.openedFiles was empty")
+		_, ok := fsCtx.OpenedFile(3)
+		require.True(t, ok, "sys.openedFiles was empty")
 
 		// Closing should not err.
 		require.NoError(t, m.Close(testCtx))
 
 		// Verify our intended side-effect
-		require.Equal(t, 0, len(sys.openedFiles), "expected no opened files")
+		_, ok = fsCtx.OpenedFile(3)
+		require.False(t, ok, "expected no opened files")
 
 		// Verify no error closing again.
 		require.NoError(t, m.Close(testCtx))
diff --git a/internal/wasm/sys.go b/internal/wasm/sys.go
index 8c921502..20977ccb 100644
--- a/internal/wasm/sys.go
+++ b/internal/wasm/sys.go
@@ -5,20 +5,9 @@ import (
 	"errors"
 	"fmt"
 	"io"
-	"io/fs"
-	"math"
-	"sync/atomic"
-)
 
-// FileEntry maps a path to an open file in a file system.
-//
-// Note: This does not introduce cycles because the types here are in the package "wasi" not "internalwasi".
-type FileEntry struct {
-	Path string
-	FS   fs.FS
-	// File when nil this is a mount like "." or "/".
-	File fs.File
-}
+	"github.com/tetratelabs/wazero/internal/fs"
+)
 
 // SysContext holds module-scoped system resources currently only used by internalwasi.
 type SysContext struct {
@@ -28,22 +17,7 @@ type SysContext struct {
 	stdout, stderr        io.Writer
 	randSource            io.Reader
 
-	// openedFiles is a map of file descriptor numbers (>=3) to open files (or directories) and defaults to empty.
-	// TODO: This is unguarded, so not goroutine-safe!
-	openedFiles map[uint32]*FileEntry
-
-	// lastFD is not meant to be read directly. Rather by nextFD.
-	lastFD uint32
-}
-
-// nextFD gets the next file descriptor number in a goroutine safe way (monotonically) or zero if we ran out.
-// TODO: opendFiles is still not goroutine safe!
-// TODO: This can return zero if we ran out of file descriptors. A future change can optimize by re-using an FD pool.
-func (c *SysContext) nextFD() uint32 {
-	if c.lastFD == math.MaxUint32 {
-		return 0
-	}
-	return atomic.AddUint32(&c.lastFD, 1)
+	fs *fs.Context
 }
 
 // Args is like os.Args and defaults to nil.
@@ -98,6 +72,13 @@ func (c *SysContext) Stderr() io.Writer {
 	return c.stderr
 }
 
+func (c *SysContext) FS() *fs.Context {
+	if c.fs == nil {
+		return &fs.Context{}
+	}
+	return c.fs
+}
+
 // RandSource is a source of random bytes and defaults to crypto/rand.Reader.
 // see wazero.ModuleConfig WithRandSource
 func (c *SysContext) RandSource() io.Reader {
@@ -129,7 +110,7 @@ var _ = DefaultSysContext() // Force panic on bug.
 
 // NewSysContext is a factory function which helps avoid needing to know defaults or exporting all fields.
 // Note: max is exposed for testing. max is only used for env/args validation.
-func NewSysContext(max uint32, args, environ []string, stdin io.Reader, stdout, stderr io.Writer, randSource io.Reader, openedFiles map[uint32]*FileEntry) (sys *SysContext, err error) {
+func NewSysContext(max uint32, args, environ []string, stdin io.Reader, stdout, stderr io.Writer, randSource io.Reader, openedFiles map[uint32]*fs.FileEntry) (sys *SysContext, err error) {
 	sys = &SysContext{args: args, environ: environ}
 
 	if sys.argsSize, err = nullTerminatedByteCount(max, args); err != nil {
@@ -164,18 +145,8 @@ func NewSysContext(max uint32, args, environ []string, stdin io.Reader, stdout,
 		sys.randSource = randSource
 	}
 
-	if openedFiles == nil {
-		sys.openedFiles = map[uint32]*FileEntry{}
-		sys.lastFD = 2 // STDERR
-	} else {
-		sys.openedFiles = openedFiles
-		sys.lastFD = 2 // STDERR
-		for fd := range openedFiles {
-			if fd > sys.lastFD {
-				sys.lastFD = fd
-			}
-		}
-	}
+	sys.fs = fs.NewContext(openedFiles)
+
 	return
 }
 
@@ -207,50 +178,3 @@ func nullTerminatedByteCount(max uint32, elements []string) (uint32, error) {
 	}
 	return uint32(bufSize), nil
 }
-
-// Close implements io.Closer
-func (c *SysContext) Close() (err error) {
-	// Close any files opened in this context
-	for fd, entry := range c.openedFiles {
-		delete(c.openedFiles, fd)
-		if entry.File != nil { // File is nil for a mount like "." or "/"
-			if e := entry.File.Close(); e != nil {
-				err = e // This means the err returned == the last non-nil error.
-			}
-		}
-	}
-	return
-}
-
-// CloseFile returns true if a file was opened and closed without error, or false if not.
-func (c *SysContext) CloseFile(fd uint32) (bool, error) {
-	f, ok := c.openedFiles[fd]
-	if !ok {
-		return false, nil
-	}
-	delete(c.openedFiles, fd)
-
-	if f.File == nil { // TODO: currently, this means it is a pre-opened filesystem, but this may change later.
-		return true, nil
-	}
-	if err := f.File.Close(); err != nil {
-		return false, err
-	}
-	return true, nil
-}
-
-// OpenedFile returns a file and true if it was opened or nil and false, if not.
-func (c *SysContext) OpenedFile(fd uint32) (*FileEntry, bool) {
-	f, ok := c.openedFiles[fd]
-	return f, ok
-}
-
-// OpenFile returns the file descriptor of the new file or false if we ran out of file descriptors
-func (c *SysContext) OpenFile(f *FileEntry) (uint32, bool) {
-	newFD := c.nextFD()
-	if newFD == 0 {
-		return 0, false
-	}
-	c.openedFiles[newFD] = f
-	return newFD, true
-}
diff --git a/internal/wasm/sys_test.go b/internal/wasm/sys_test.go
index 3de8399a..52b08953 100644
--- a/internal/wasm/sys_test.go
+++ b/internal/wasm/sys_test.go
@@ -3,11 +3,7 @@ package wasm
 import (
 	"bytes"
 	"io"
-	"io/fs"
-	"os"
-	"path"
 	"testing"
-	"testing/fstest"
 
 	"github.com/tetratelabs/wazero/internal/testing/require"
 )
@@ -32,8 +28,6 @@ func TestDefaultSysContext(t *testing.T) {
 	require.Equal(t, eofReader{}, sys.Stdin())
 	require.Equal(t, io.Discard, sys.Stdout())
 	require.Equal(t, io.Discard, sys.Stderr())
-	require.Equal(t, 0, len(sys.openedFiles), "expected no opened files")
-
 	require.Equal(t, sys, DefaultSysContext())
 }
 
@@ -154,108 +148,3 @@ func TestNewSysContext_Environ(t *testing.T) {
 		})
 	}
 }
-
-func TestSysContext_Close(t *testing.T) {
-	t.Run("no files", func(t *testing.T) {
-		sys := DefaultSysContext()
-		require.NoError(t, sys.Close())
-	})
-
-	t.Run("open files", func(t *testing.T) {
-		tempDir := t.TempDir()
-		pathName := "test"
-		file, testFS := createWriteableFile(t, tempDir, pathName, make([]byte, 0))
-
-		sys, err := NewSysContext(
-			0,   // max
-			nil, // args
-			nil, // environ
-			nil, // stdin
-			nil, // stdout
-			nil, // stderr
-			nil, // randSource
-			map[uint32]*FileEntry{ // openedFiles
-				3: {Path: "/", FS: testFS},
-				4: {Path: ".", FS: testFS},
-				5: {Path: path.Join(".", pathName), File: file, FS: testFS},
-			},
-		)
-		require.NoError(t, err)
-
-		// Closing should delete the file descriptors after closing the files.
-		require.NoError(t, sys.Close())
-		require.Equal(t, 0, len(sys.openedFiles), "expected no opened files")
-
-		// Verify it was actually closed, by trying to close it again.
-		err = file.(*os.File).Close()
-		require.Contains(t, err.Error(), "file already closed")
-
-		// No problem closing config again because the descriptors were removed, so they won't be called again.
-		require.NoError(t, sys.Close())
-	})
-
-	t.Run("FS never used", func(t *testing.T) {
-		testFS := fstest.MapFS{}
-		sys, err := NewSysContext(
-			0,   // max
-			nil, // args
-			nil, // environ
-			nil, // stdin
-			nil, // stdout
-			nil, // stderr
-			nil, // randSource
-			map[uint32]*FileEntry{ // no openedFiles
-				3: {Path: "/", FS: testFS},
-				4: {Path: ".", FS: testFS},
-			},
-		)
-		require.NoError(t, err)
-
-		// Even if there are no open files, the descriptors for the file-system mappings should be removed.
-		require.NoError(t, sys.Close())
-		require.Equal(t, 0, len(sys.openedFiles), "expected no opened files")
-	})
-
-	t.Run("open file externally closed", func(t *testing.T) {
-		tempDir := t.TempDir()
-		pathName := "test"
-		file, testFS := createWriteableFile(t, tempDir, pathName, make([]byte, 0))
-
-		sys, err := NewSysContext(
-			0,   // max
-			nil, // args
-			nil, // environ
-			nil, // stdin
-			nil, // stdout
-			nil, // stderr
-			nil, // randSource
-			map[uint32]*FileEntry{ // openedFiles
-				3: {Path: "/", FS: testFS},
-				4: {Path: ".", FS: testFS},
-				5: {Path: path.Join(".", pathName), File: file, FS: testFS},
-			},
-		)
-		require.NoError(t, err)
-
-		// Close the file externally
-		file.Close()
-
-		// Closing should err as it expected to be open
-		require.Contains(t, sys.Close().Error(), "file already closed")
-
-		// However, cleanup should still occur.
-		require.Equal(t, 0, len(sys.openedFiles), "expected no opened files")
-	})
-}
-
-// createWriteableFile uses real files when io.Writer tests are needed.
-func createWriteableFile(t *testing.T, tmpDir string, pathName string, data []byte) (fs.File, fs.FS) {
-	require.NotNil(t, data)
-	absolutePath := path.Join(tmpDir, pathName)
-	require.NoError(t, os.WriteFile(absolutePath, data, 0o600))
-
-	// open the file for writing in a custom way until #390
-	f, err := os.OpenFile(absolutePath, os.O_RDWR, 0o600)
-	require.NoError(t, err)
-	return f, os.DirFS(tmpDir)
-}
diff --git a/wasi/wasi.go b/wasi/wasi.go
index 0c758c7e..a6a8cd0f 100644
--- a/wasi/wasi.go
+++ b/wasi/wasi.go
@@ -16,6 +16,7 @@ import (
 	"github.com/tetratelabs/wazero"
 	"github.com/tetratelabs/wazero/api"
 	"github.com/tetratelabs/wazero/experimental"
+	internalfs "github.com/tetratelabs/wazero/internal/fs"
 	"github.com/tetratelabs/wazero/internal/wasm"
 )
 
@@ -691,9 +692,9 @@ func (a *snapshotPreview1) FdAllocate(ctx context.Context, m api.Module, fd uint
 // See https://github.com/WebAssembly/WASI/blob/main/phases/snapshot/docs.md#fd_close
 // See https://linux.die.net/man/3/close
 func (a *snapshotPreview1) FdClose(ctx context.Context, m api.Module, fd uint32) Errno {
-	sys := sysCtx(m)
+	_, fsc := sysFSCtx(ctx, m)
 
-	if ok, err := sys.CloseFile(fd); err != nil {
+	if ok, err := fsc.CloseFile(fd); err != nil {
 		return ErrnoIo
 	} else if !ok {
 		return ErrnoBadf
@@ -740,9 +741,9 @@ func (a *snapshotPreview1) FdDatasync(ctx context.Context, m api.Module, fd uint
 // See https://github.com/WebAssembly/WASI/blob/main/phases/snapshot/docs.md#fd_fdstat_get
 // See https://linux.die.net/man/3/fsync
 func (a *snapshotPreview1) FdFdstatGet(ctx context.Context, m api.Module, fd uint32, resultStat uint32) Errno {
-	sys := sysCtx(m)
+	_, fsc := sysFSCtx(ctx, m)
 
-	if _, ok := sys.OpenedFile(fd); !ok {
+	if _, ok := fsc.OpenedFile(fd); !ok {
 		return ErrnoBadf
 	}
 	return ErrnoSuccess
@@ -776,9 +777,9 @@ func (a *snapshotPreview1) FdFdstatGet(ctx context.Context, m api.Module, fd uin
 // See https://github.com/WebAssembly/WASI/blob/snapshot-01/phases/snapshot/docs.md#prestat
 // See https://github.com/WebAssembly/WASI/blob/main/phases/snapshot/docs.md#fd_prestat_get
 func (a *snapshotPreview1) FdPrestatGet(ctx context.Context, m api.Module, fd uint32, resultPrestat uint32) Errno {
-	sys := sysCtx(m)
+	_, fsc := sysFSCtx(ctx, m)
 
-	entry, ok := sys.OpenedFile(fd)
+	entry, ok := fsc.OpenedFile(fd)
 	if !ok {
 		return ErrnoBadf
 	}
@@ -851,9 +852,9 @@ func (a *snapshotPreview1) FdPread(ctx context.Context, m api.Module, fd, iovs,
 // See FdPrestatGet
 // See https://github.com/WebAssembly/WASI/blob/snapshot-01/phases/snapshot/docs.md#fd_prestat_dir_name
 func (a *snapshotPreview1) FdPrestatDirName(ctx context.Context, m api.Module, fd uint32, pathPtr uint32, pathLen uint32) Errno {
-	sys := sysCtx(m)
+	_, fsc := sysFSCtx(ctx, m)
 
-	f, ok := sys.OpenedFile(fd)
+	f, ok := fsc.OpenedFile(fd)
 	if !ok {
 		return ErrnoBadf
 	}
@@ -919,13 +920,13 @@ func (a *snapshotPreview1) FdPwrite(ctx context.Context, m api.Module, fd, iovs,
 // See https://github.com/WebAssembly/WASI/blob/snapshot-01/phases/snapshot/docs.md#iovec
 // See https://linux.die.net/man/3/readv
 func (a *snapshotPreview1) FdRead(ctx context.Context, m api.Module, fd, iovs, iovsCount, resultSize uint32) Errno {
-	sys := sysCtx(m)
+	sys, fsc := sysFSCtx(ctx, m)
 
 	var reader io.Reader
 
 	if fd == fdStdin {
 		reader = sys.Stdin()
-	} else if f, ok := sys.OpenedFile(fd); !ok || f.File == nil {
+	} else if f, ok := fsc.OpenedFile(fd); !ok || f.File == nil {
 		return ErrnoBadf
 	} else {
 		reader = f.File
@@ -1002,11 +1003,11 @@ func (a *snapshotPreview1) FdRenumber(ctx context.Context, m api.Module, fd, to
 // See https://github.com/WebAssembly/WASI/blob/snapshot-01/phases/snapshot/docs.md#fd_seek
 // See https://linux.die.net/man/3/lseek
 func (a *snapshotPreview1) FdSeek(ctx context.Context, m api.Module, fd uint32, offset uint64, whence uint32, resultNewoffset uint32) Errno {
-	sys := sysCtx(m)
+	_, fsc := sysFSCtx(ctx, m)
 
 	var seeker io.Seeker
 	// Check to see if the file descriptor is available
-	if f, ok := sys.OpenedFile(fd); !ok || f.File == nil {
+	if f, ok := fsc.OpenedFile(fd); !ok || f.File == nil {
 		return ErrnoBadf
 		// fs.FS doesn't declare io.Seeker, but implementations such as os.File implement it.
 	} else if seeker, ok = f.File.(io.Seeker); !ok {
@@ -1088,7 +1089,7 @@ func (a *snapshotPreview1) FdTell(ctx context.Context, m api.Module, fd, resultO
 // See https://github.com/WebAssembly/WASI/blob/snapshot-01/phases/snapshot/docs.md#fd_write
 // See https://linux.die.net/man/3/writev
 func (a *snapshotPreview1) FdWrite(ctx context.Context, m api.Module, fd, iovs, iovsCount, resultSize uint32) Errno {
-	sys := sysCtx(m)
+	sys, fsc := sysFSCtx(ctx, m)
 
 	var writer io.Writer
 
@@ -1099,7 +1100,7 @@ func (a *snapshotPreview1) FdWrite(ctx context.Context, m api.Module, fd, iovs,
 		writer = sys.Stderr()
 	default:
 		// Check to see if the file descriptor is available
-		if f, ok := sys.OpenedFile(fd); !ok || f.File == nil {
+		if f, ok := fsc.OpenedFile(fd); !ok || f.File == nil {
 			return ErrnoBadf
 			// fs.FS doesn't declare io.Writer, but implementations such as os.File implement it.
 		} else if writer, ok = f.File.(io.Writer); !ok {
@@ -1201,9 +1202,9 @@ func (a *snapshotPreview1) PathLink(ctx context.Context, m api.Module, oldFd, ol
 // See https://linux.die.net/man/3/openat
 func (a *snapshotPreview1) PathOpen(ctx context.Context, m api.Module, fd, dirflags, pathPtr, pathLen, oflags uint32, fsRightsBase,
 	fsRightsInheriting uint64, fdflags, resultOpenedFd uint32) (errno Errno) {
-	sys := sysCtx(m)
+	_, fsc := sysFSCtx(ctx, m)
 
-	dir, ok := sys.OpenedFile(fd)
+	dir, ok := fsc.OpenedFile(fd)
 	if !ok || dir.FS == nil {
 		return ErrnoBadf
 	}
@@ -1221,7 +1222,7 @@ func (a *snapshotPreview1) PathOpen(ctx context.Context, m api.Module, fd, dirfl
 		return errno
 	}
 
-	if newFD, ok := sys.OpenFile(entry); !ok {
+	if newFD, ok := fsc.OpenFile(entry); !ok {
 		_ = entry.File.Close()
 		return ErrnoIo
 	} else if !m.Memory().WriteUint32Le(ctx, resultOpenedFd, newFD) {
@@ -1362,7 +1363,23 @@ func sysCtx(m api.Module) *wasm.SysContext {
 	}
 }
 
-func openFileEntry(rootFS fs.FS, pathName string) (*wasm.FileEntry, Errno) {
+func sysFSCtx(ctx context.Context, m api.Module) (*wasm.SysContext, *internalfs.Context) {
+	if internal, ok := m.(*wasm.CallContext); !ok {
+		panic(fmt.Errorf("unsupported wasm.Module implementation: %v", m))
+	} else {
+		// Override Context when it is passed via context
+		if fsValue := ctx.Value(internalfs.Key{}); fsValue != nil {
+			fsCtx, ok := fsValue.(*internalfs.Context)
+			if !ok {
+				panic(fmt.Errorf("unsupported fs key: %v", fsValue))
+			}
+			return internal.Sys, fsCtx
+		}
+		return internal.Sys, internal.Sys.FS()
+	}
+}
+
+func openFileEntry(rootFS fs.FS, pathName string) (*internalfs.FileEntry, Errno) {
 	f, err := rootFS.Open(pathName)
 	if err != nil {
 		switch {
@@ -1378,7 +1395,7 @@ func openFileEntry(rootFS fs.FS, pathName string) (*wasm.FileEntry, Errno) {
 	// TODO: verify if oflags is a directory and fail with wasi.ErrnoNotdir if not
 	// See https://github.com/WebAssembly/WASI/blob/snapshot-01/phases/snapshot/docs.md#-oflags-flagsu16
 
-	return &wasm.FileEntry{Path: pathName, FS: rootFS, File: f}, ErrnoSuccess
+	return &internalfs.FileEntry{Path: pathName, FS: rootFS, File: f}, ErrnoSuccess
 }
 
 func writeOffsetsAndNullTerminatedValues(ctx context.Context, mem api.Memory, values []string, offsets, bytes uint32) Errno {
diff --git a/wasi/wasi_test.go b/wasi/wasi_test.go
index 88cedc45..2f92a7e4 100644
--- a/wasi/wasi_test.go
+++ b/wasi/wasi_test.go
@@ -19,6 +19,7 @@ import (
 	"github.com/tetratelabs/wazero"
 	"github.com/tetratelabs/wazero/api"
 	"github.com/tetratelabs/wazero/experimental"
+	fs2 "github.com/tetratelabs/wazero/internal/fs"
 	"github.com/tetratelabs/wazero/internal/testing/require"
 	"github.com/tetratelabs/wazero/internal/wasm"
 	"github.com/tetratelabs/wazero/sys"
@@ -546,7 +547,7 @@ func TestSnapshotPreview1_FdClose(t *testing.T) {
 		entry2, errno := openFileEntry(testFs, path2)
 		require.Zero(t, errno, ErrnoName(errno))
 
-		sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+		sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 			fdToClose: entry1,
 			fdToKeep:  entry2,
 		})
@@ -558,11 +559,12 @@ func TestSnapshotPreview1_FdClose(t *testing.T) {
 
 	verify := func(mod api.Module) {
 		// Verify fdToClose is closed and removed from the opened FDs.
-		_, ok := sysCtx(mod).OpenedFile(fdToClose)
+		_, fsc := sysFSCtx(testCtx, mod)
+		_, ok := fsc.OpenedFile(fdToClose)
 		require.False(t, ok)
 
 		// Verify fdToKeep is not closed
-		_, ok = sysCtx(mod).OpenedFile(fdToKeep)
+		_, ok = fsc.OpenedFile(fdToKeep)
 		require.True(t, ok)
 	}
 
@@ -731,7 +733,7 @@ func TestSnapshotPreview1_FdPrestatGet(t *testing.T) {
 	fd := uint32(3) // arbitrary fd after 0, 1, and 2, that are stdin/out/err
 
 	pathName := "/tmp"
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{fd: {Path: pathName}})
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{fd: {Path: pathName}})
 	require.NoError(t, err)
 
 	a, mod, fn := instantiateModule(testCtx, t, functionFdPrestatGet, importFdPrestatGet, sysCtx)
@@ -776,7 +778,7 @@ func TestSnapshotPreview1_FdPrestatGet_Errors(t *testing.T) {
 	fd := uint32(3)           // fd 3 will be opened for the "/tmp" directory after 0, 1, and 2, that are stdin/out/err
 	validAddress := uint32(0) // Arbitrary valid address as arguments to fd_prestat_get. We chose 0 here.
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{fd: {Path: "/tmp"}})
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{fd: {Path: "/tmp"}})
 	require.NoError(t, err)
 
 	a, mod, _ := instantiateModule(testCtx, t, functionFdPrestatGet, importFdPrestatGet, sysCtx)
@@ -818,7 +820,7 @@ func TestSnapshotPreview1_FdPrestatGet_Errors(t *testing.T) {
 func TestSnapshotPreview1_FdPrestatDirName(t *testing.T) {
 	fd := uint32(3) // arbitrary fd after 0, 1, and 2, that are stdin/out/err
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{fd: {Path: "/tmp"}})
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{fd: {Path: "/tmp"}})
 	require.NoError(t, err)
 
 	a, mod, fn := instantiateModule(testCtx, t, functionFdPrestatDirName, importFdPrestatDirName, sysCtx)
@@ -859,7 +861,7 @@ func TestSnapshotPreview1_FdPrestatDirName(t *testing.T) {
 
 func TestSnapshotPreview1_FdPrestatDirName_Errors(t *testing.T) {
 	fd := uint32(3) // arbitrary fd after 0, 1, and 2, that are stdin/out/err
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{fd: {Path: "/tmp"}})
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{fd: {Path: "/tmp"}})
 	require.NoError(t, err)
 
 	a, mod, _ := instantiateModule(testCtx, t, functionFdPrestatDirName, importFdPrestatDirName, sysCtx)
@@ -981,7 +983,7 @@ func TestSnapshotPreview1_FdRead(t *testing.T) {
 		t.Run(tc.name, func(t *testing.T) {
 			// Create a fresh file to read the contents from
 			file, testFS := createFile(t, "test_path", []byte("wazero"))
-			sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+			sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 				fd: {Path: "test_path", FS: testFS, File: file},
 			})
 			require.NoError(t, err)
@@ -1008,7 +1010,7 @@ func TestSnapshotPreview1_FdRead_Errors(t *testing.T) {
 	validFD := uint32(3)                                 // arbitrary valid fd after 0, 1, and 2, that are stdin/out/err
 	file, testFS := createFile(t, "test_path", []byte{}) // file with empty contents
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 		validFD: {Path: "test_path", FS: testFS, File: file},
 	})
 	require.NoError(t, err)
@@ -1137,11 +1139,13 @@ func TestSnapshotPreview1_FdSeek(t *testing.T) {
 	resultNewoffset := uint32(1)                                 // arbitrary offset in `ctx.Memory` for the new offset value
 	file, testFS := createFile(t, "test_path", []byte("wazero")) // arbitrary non-empty contents
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 		fd: {Path: "test_path", FS: testFS, File: file},
 	})
 	require.NoError(t, err)
 
+	fsCtx := sysCtx.FS()
+
 	a, mod, fn := instantiateModule(testCtx, t, functionFdSeek, importFdSeek, sysCtx)
 	defer mod.Close(testCtx)
 
@@ -1214,7 +1218,7 @@ func TestSnapshotPreview1_FdSeek(t *testing.T) {
 					maskMemory(t, testCtx, mod, len(tc.expectedMemory))
 
 					// Since we initialized this file, we know it is a seeker (because it is a MapFile)
-					f, ok := sysCtx.OpenedFile(fd)
+					f, ok := fsCtx.OpenedFile(fd)
 					require.True(t, ok)
 					seeker := f.File.(io.Seeker)
 
@@ -1243,7 +1247,7 @@ func TestSnapshotPreview1_FdSeek_Errors(t *testing.T) {
 	validFD := uint32(3)                                         // arbitrary valid fd after 0, 1, and 2, that are stdin/out/err
 	file, testFS := createFile(t, "test_path", []byte("wazero")) // arbitrary valid file with non-empty contents
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 		validFD: {Path: "test_path", FS: testFS, File: file},
 	})
 	require.NoError(t, err)
@@ -1374,7 +1378,7 @@ func TestSnapshotPreview1_FdWrite(t *testing.T) {
 			// Create a fresh file to write the contents to
 			pathName := "test_path"
 			file, testFS := createWriteableFile(t, tmpDir, pathName, []byte{})
-			sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+			sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 				fd: {Path: pathName, FS: testFS, File: file},
 			})
 			require.NoError(t, err)
@@ -1409,7 +1413,7 @@ func TestSnapshotPreview1_FdWrite_Errors(t *testing.T) {
 	pathName := "test_path"
 	file, testFS := createWriteableFile(t, tmpDir, pathName, []byte{})
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 		validFD: {Path: pathName, FS: testFS, File: file},
 	})
 	require.NoError(t, err)
@@ -1553,32 +1557,44 @@ func TestSnapshotPreview1_PathLink(t *testing.T) {
 }
 
 func TestSnapshotPreview1_PathOpen(t *testing.T) {
-	workdirFD := uint32(3) // arbitrary fd after 0, 1, and 2, that are stdin/out/err
-	dirflags := uint32(0)  // arbitrary dirflags
-	oflags := uint32(0)    // arbitrary oflags
-	fdFlags := uint32(0)
+	type pathOpenArgs struct {
+		fd                 uint32
+		dirflags           uint32
+		pathPtr            uint32
+		pathLen            uint32
+		oflags             uint32
+		fsRightsBase       uint64
+		fsRightsInheriting uint64
+		fdflags            uint32
+		resultOpenedFd     uint32
+	}
 
-	// Setup the initial memory to include the path name starting at an offset.
-	pathName := "wazero"
-	path := uint32(1)
-	pathLen := uint32(len(pathName))
-	initialMemory := append([]byte{'?'}, pathName...)
+	setup := func(workdirFD uint32, pathName string) (*snapshotPreview1, api.Module, api.Function, pathOpenArgs, []byte, uint32) {
+		// Setup the initial memory to include the path name starting at an offset.
+		initialMemory := append([]byte{'?'}, pathName...)
 
-	expectedFD := byte(workdirFD + 1)
-	resultOpenedFd := uint32(len(initialMemory) + 1)
-	expectedMemory := append(
-		initialMemory,
-		'?', // `resultOpenedFd` is after this
-		expectedFD, 0, 0, 0,
-		'?',
-	)
+		expectedFD := workdirFD + 1
+		expectedMemory := append(
+			initialMemory,
+			'?', // `resultOpenedFd` is after this
+			byte(expectedFD), 0, 0, 0,
+			'?',
+		)
 
-	// rights are ignored per https://github.com/WebAssembly/WASI/issues/469#issuecomment-1045251844
-	fsRightsBase, fsRightsInheriting := uint64(1), uint64(2)
+		args := pathOpenArgs{
+			fd:                 workdirFD,
+			dirflags:           0,
+			pathPtr:            1,
+			pathLen:            uint32(len(pathName)),
+			oflags:             0,
+			fsRightsBase:       1, // rights are ignored per https://github.com/WebAssembly/WASI/issues/469#issuecomment-1045251844
+			fsRightsInheriting: 2,
+			fdflags:            0,
+			resultOpenedFd:     uint32(len(initialMemory) + 1),
+		}
 
-	setup := func() (*snapshotPreview1, api.Module, api.Function) {
 		testFS := fstest.MapFS{pathName: &fstest.MapFile{Mode: os.ModeDir}}
-		sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+		sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 			workdirFD: {Path: ".", FS: testFS},
 		})
 		require.NoError(t, err)
@@ -1586,10 +1602,10 @@ func TestSnapshotPreview1_PathOpen(t *testing.T) {
 		maskMemory(t, testCtx, mod, len(expectedMemory))
 		ok := mod.Memory().Write(testCtx, 0, initialMemory)
 		require.True(t, ok)
-		return a, mod, fn
+		return a, mod, fn, args, expectedMemory, expectedFD
 	}
 
-	verify := func(errno Errno, mod api.Module) {
+	verify := func(ctx context.Context, errno Errno, mod api.Module, pathName string, expectedMemory []byte, expectedFD uint32) {
 		require.Zero(t, errno, ErrnoName(errno))
 
 		actual, ok := mod.Memory().Read(testCtx, 0, uint32(len(expectedMemory)))
@@ -1597,23 +1613,55 @@ func TestSnapshotPreview1_PathOpen(t *testing.T) {
 		require.Equal(t, expectedMemory, actual)
 
 		// verify the file was actually opened
-		f, ok := sysCtx(mod).OpenedFile(uint32(expectedFD))
+		_, fsc := sysFSCtx(ctx, mod)
+		f, ok := fsc.OpenedFile(expectedFD)
 		require.True(t, ok)
 		require.Equal(t, pathName, f.Path)
 	}
 
 	t.Run("snapshotPreview1.PathOpen", func(t *testing.T) {
-		a, mod, _ := setup()
-		errno := a.PathOpen(testCtx, mod, workdirFD, dirflags, path, pathLen, oflags, fsRightsBase, fsRightsInheriting, fdFlags, resultOpenedFd)
-		verify(errno, mod)
+		workdirFD := uint32(3) // arbitrary fd after 0, 1, and 2, that are stdin/out/err
+		pathName := "wazero"
+
+		a, mod, _, args, expectedMemory, expectedFD := setup(workdirFD, pathName)
+		errno := a.PathOpen(testCtx, mod, args.fd, args.dirflags, args.pathPtr, args.pathLen, args.oflags,
+			args.fsRightsBase, args.fsRightsInheriting, args.fdflags, args.resultOpenedFd)
+		verify(testCtx, errno, mod, pathName, expectedMemory, expectedFD)
 	})
 
 	t.Run(functionPathOpen, func(t *testing.T) {
-		_, mod, fn := setup()
-		results, err := fn.Call(testCtx, uint64(workdirFD), uint64(dirflags), uint64(path), uint64(pathLen), uint64(oflags), fsRightsBase, fsRightsInheriting, uint64(fdFlags), uint64(resultOpenedFd))
+		workdirFD := uint32(3) // arbitrary fd after 0, 1, and 2, that are stdin/out/err
+		pathName := "wazero"
+
+		_, mod, fn, args, expectedMemory, expectedFD := setup(workdirFD, pathName)
+		results, err := fn.Call(testCtx, uint64(args.fd), uint64(args.dirflags), uint64(args.pathPtr), uint64(args.pathLen),
+			uint64(args.oflags), args.fsRightsBase, args.fsRightsInheriting, uint64(args.fdflags), uint64(args.resultOpenedFd))
 		require.NoError(t, err)
 		errno := Errno(results[0])
-		verify(errno, mod)
+		verify(testCtx, errno, mod, pathName, expectedMemory, expectedFD)
+	})
+
+	t.Run("snapshotPreview1.PathOpen.WithFS", func(t *testing.T) {
+		workdirFD := uint32(100) // dummy fd as it is not used
+		pathName := "wazero"
+
+		// The filesystem initialized in setup() is not used as it will be overridden.
+		a, mod, _, args, expectedMemory, _ := setup(workdirFD, pathName)
+
+		// Override fs.FS through context
+		workdirFD = uint32(4) // 3 is '/' and 4 is '.'
+		expectedFD := workdirFD + 1
+		expectedMemory[8] = byte(expectedFD) // replace expected memory with expected fd
+		testFS := fstest.MapFS{pathName: &fstest.MapFile{Mode: os.ModeDir}}
+		ctx, closer, err := experimental.WithFS(testCtx, testFS)
+		require.NoError(t, err)
+		defer closer.Close(ctx)
+
+		errno := a.PathOpen(ctx, mod, workdirFD, args.dirflags, args.pathPtr, args.pathLen, args.oflags,
+			args.fsRightsBase, args.fsRightsInheriting, args.fdflags, args.resultOpenedFd)
+		require.Zero(t, errno, ErrnoName(errno))
+
+		verify(ctx, errno, mod, pathName, expectedMemory, expectedFD)
 	})
 }
 
@@ -1622,7 +1670,7 @@ func TestSnapshotPreview1_PathOpen_Errors(t *testing.T) {
 	pathName := "wazero"
 	testFS := fstest.MapFS{pathName: &fstest.MapFile{Mode: os.ModeDir}}
 
-	sysCtx, err := newSysContext(nil, nil, map[uint32]*wasm.FileEntry{
+	sysCtx, err := newSysContext(nil, nil, map[uint32]*fs2.FileEntry{
 		validFD: {Path: ".", FS: testFS},
 	})
 	require.NoError(t, err)
@@ -2076,7 +2124,7 @@ func instantiateModule(ctx context.Context, t *testing.T, wasifunction, wasiimpo
 	return a, mod, fn
 }
 
-func newSysContext(args, environ []string, openedFiles map[uint32]*wasm.FileEntry) (sysCtx *wasm.SysContext, err error) {
+func newSysContext(args, environ []string, openedFiles map[uint32]*fs2.FileEntry) (sysCtx *wasm.SysContext, err error) {
 	return wasm.NewSysContext(math.MaxUint32, args, environ, new(bytes.Buffer), nil, nil, nil, openedFiles)
 }