diff --git a/go/ai/_test_data/prompts/example.prompt b/go/ai/_test_data/prompts/example.prompt
new file mode 100644
index 0000000000..c47c70b4fc
--- /dev/null
+++ b/go/ai/_test_data/prompts/example.prompt
@@ -0,0 +1,20 @@
+---
+model: test-model
+maxTurns: 5
+description: A test prompt
+toolChoice: required
+returnToolRequests: true
+input:
+  schema:
+    type: object
+    properties:
+      name:
+        type: string
+  default:
+    name: world
+output:
+  format: text
+  schema:
+    type: string
+---
+Hello, {{name}}!
\ No newline at end of file
diff --git a/go/ai/prompt.go b/go/ai/prompt.go
index 95214dd7a6..b2932f2720 100644
--- a/go/ai/prompt.go
+++ b/go/ai/prompt.go
@@ -18,6 +18,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io/fs"
 	"log/slog"
 	"maps"
 	"os"
@@ -505,12 +506,17 @@ func LoadPromptDir(r api.Registry, dir string, namespace string) {
 		return
 	}
 
-	loadPromptDir(r, path, namespace)
+	loadPromptDir(r, os.DirFS(dir), ".", namespace)
+}
+
+// LoadPromptFS loads prompts and partials from the given filesystem for the given namespace.
+func LoadPromptFS(r api.Registry, fsys fs.FS, dir string, namespace string) {
+	loadPromptDir(r, fsys, dir, namespace)
 }
 
 // loadPromptDir recursively loads prompts and partials from the directory.
-func loadPromptDir(r api.Registry, dir string, namespace string) {
-	entries, err := os.ReadDir(dir)
+func loadPromptDir(r api.Registry, fsys fs.FS, dir, namespace string) {
+	entries, err := fs.ReadDir(fsys, dir)
 	if err != nil {
 		panic(fmt.Errorf("failed to read prompt directory structure: %w", err))
 	}
@@ -519,7 +525,7 @@ func loadPromptDir(r api.Registry, dir string, namespace string) {
 		filename := entry.Name()
 		path := filepath.Join(dir, filename)
 		if entry.IsDir() {
-			loadPromptDir(r, path, namespace)
+			loadPromptDir(r, fsys, path, namespace)
 		} else if strings.HasSuffix(filename, ".prompt") {
 			if strings.HasPrefix(filename, "_") {
 				partialName := strings.TrimSuffix(filename[1:], ".prompt")
@@ -531,7 +537,7 @@ func loadPromptDir(r api.Registry, dir string, namespace string) {
 				r.RegisterPartial(partialName, string(source))
 				slog.Debug("Registered Dotprompt partial", "name", partialName, "file", path)
 			} else {
-				LoadPrompt(r, dir, filename, namespace)
+				loadPrompt(r, fsys, dir, filename, namespace)
 			}
 		}
 	}
@@ -539,11 +545,17 @@ func loadPromptDir(r api.Registry, dir string, namespace string) {
 
 // LoadPrompt loads a single prompt into the registry.
 func LoadPrompt(r api.Registry, dir, filename, namespace string) Prompt {
+	dir, rest := filepath.Split(dir)
+	return loadPrompt(r, os.DirFS(dir), rest, filename, namespace)
+}
+
+// loadPrompt uses provided fsys to load a single prompt into the registry.
+func loadPrompt(r api.Registry, fsys fs.FS, dir, filename, namespace string) Prompt {
 	name := strings.TrimSuffix(filename, ".prompt")
 	name, variant, _ := strings.Cut(name, ".")
 
 	sourceFile := filepath.Join(dir, filename)
-	source, err := os.ReadFile(sourceFile)
+	source, err := fs.ReadFile(fsys, sourceFile)
 	if err != nil {
 		slog.Error("Failed to read prompt file", "file", sourceFile, "error", err)
 		return nil
diff --git a/go/ai/prompt_test.go b/go/ai/prompt_test.go
index be1f6c1354..008b0d811c 100644
--- a/go/ai/prompt_test.go
+++ b/go/ai/prompt_test.go
@@ -16,6 +16,7 @@ package ai
 
 import (
 	"context"
+	"embed"
 	"fmt"
 	"os"
 	"path/filepath"
@@ -29,6 +30,9 @@ import (
 	"github.com/google/go-cmp/cmp/cmpopts"
 )
 
+//go:embed _test_data/prompts
+var embededPrompts embed.FS
+
 type InputOutput struct {
 	Text string `json:"text"`
 }
@@ -877,6 +881,15 @@ func assertResponse(t *testing.T, resp *ModelResponse, want string) {
 	}
 }
 
+func TestLoadPrompt_FromFS(t *testing.T) {
+	reg := registry.New()
+	LoadPromptFS(reg, embededPrompts, "_test_data/prompts", "test-namespace")
+	prompt := LookupPrompt(reg, "test-namespace/example")
+	if prompt == nil {
+		t.Fatalf("Prompt was not registered")
+	}
+}
+
 func TestLoadPrompt(t *testing.T) {
 	// Create a temporary directory for testing
 	tempDir := t.TempDir()
diff --git a/go/genkit/genkit.go b/go/genkit/genkit.go
index 83cd33afeb..2ec88fd036 100644
--- a/go/genkit/genkit.go
+++ b/go/genkit/genkit.go
@@ -21,6 +21,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io/fs"
 	"log/slog"
 	"os"
 	"os/signal"
@@ -46,6 +47,7 @@ type Genkit struct {
 type genkitOptions struct {
 	DefaultModel string       // Default model to use if no other model is specified.
 	PromptDir    string       // Directory where dotprompts are stored. Will be loaded automatically on initialization.
+	PromptFS     fs.FS        // Filesystem that will be used for PromptDir lookup.
 	Plugins      []api.Plugin // Plugin to initialize automatically.
 }
 
@@ -69,6 +71,13 @@ func (o *genkitOptions) apply(gOpts *genkitOptions) error {
 		gOpts.PromptDir = o.PromptDir
 	}
 
+	if o.PromptFS != nil {
+		if gOpts.PromptFS != nil {
+			return errors.New("cannot set prompt filesystem more than once (WithPromptFS)")
+		}
+		gOpts.PromptFS = o.PromptFS
+	}
+
 	if len(o.Plugins) > 0 {
 		if gOpts.Plugins != nil {
 			return errors.New("cannot set plugins more than once (WithPlugins)")
@@ -106,6 +115,12 @@ func WithPromptDir(dir string) GenkitOption {
 	return &genkitOptions{PromptDir: dir}
 }
 
+// WithPromptFS is a more generic version of `WithPromptDir` and accepts a filesytem
+// instead of directory path
+func WithPromptFS(fsys fs.FS) GenkitOption {
+	return &genkitOptions{PromptFS: fsys}
+}
+
 // Init creates and initializes a new [Genkit] instance with the provided options.
 // It sets up the registry, initializes plugins ([WithPlugins]), loads prompts
 // ([WithPromptDir]), and configures other settings like the default model
@@ -184,7 +199,11 @@ func Init(ctx context.Context, opts ...GenkitOption) *Genkit {
 
 	ai.ConfigureFormats(r)
 	ai.DefineGenerateAction(ctx, r)
-	ai.LoadPromptDir(r, gOpts.PromptDir, "")
+	if gOpts.PromptFS == nil {
+		ai.LoadPromptDir(r, gOpts.PromptDir, "")
+	} else {
+		ai.LoadPromptFS(r, gOpts.PromptFS, gOpts.PromptDir, "")
+	}
 
 	r.RegisterValue(api.DefaultModelKey, gOpts.DefaultModel)
 	r.RegisterValue(api.PromptDirKey, gOpts.PromptDir)
diff --git a/go/samples/prompts-dir/main.go b/go/samples/prompts-dir/main.go
index 59e5e83843..a5e15113bf 100644
--- a/go/samples/prompts-dir/main.go
+++ b/go/samples/prompts-dir/main.go
@@ -6,6 +6,7 @@ package main
 
 import (
 	"context"
+	"embed"
 	"errors"
 
 	// Import Genkit and the Google AI plugin
@@ -14,12 +15,17 @@ import (
 	"github.com/firebase/genkit/go/plugins/googlegenai"
 )
 
+//go:embed prompts
+var prompts embed.FS
+
 func main() {
 	ctx := context.Background()
 
 	g := genkit.Init(ctx,
 		genkit.WithPlugins(&googlegenai.GoogleAI{}),
 		genkit.WithPromptDir("prompts"),
+		// Without it OS's filesystem will be used
+		genkit.WithPromptFS(prompts),
 	)
 
 	type greetingStyle struct {