diff --git a/cmd/apps/init.go b/cmd/apps/init.go
index 1d5c30efb5..091de6ac00 100644
--- a/cmd/apps/init.go
+++ b/cmd/apps/init.go
@@ -792,14 +792,6 @@ func runCreate(ctx context.Context, opts createOptions) error {
 		absOutputDir = destDir
 	}
 
-	// Apply plugin-specific post-processing (e.g., remove config/queries if analytics not selected)
-	runErr = prompt.RunWithSpinnerCtx(ctx, "Configuring plugins...", func() error {
-		return applyPlugins(absOutputDir, selectedPlugins)
-	})
-	if runErr != nil {
-		return runErr
-	}
-
 	// Initialize project based on type (Node.js, Python, etc.)
 	var nextStepsCmd string
 	projectInitializer := initializer.GetProjectInitializer(absOutputDir)
@@ -946,34 +938,6 @@ func buildPluginStrings(pluginNames []string) (pluginImport, pluginUsage string)
 	return pluginImport, pluginUsage
 }
 
-// pluginOwnedPaths maps plugin names to directories they own.
-// When a plugin is not selected, its owned paths are removed from the project.
-var pluginOwnedPaths = map[string][]string{
-	"analytics": {"config/queries"},
-}
-
-// applyPlugins removes directories owned by unselected plugins.
-func applyPlugins(projectDir string, pluginNames []string) error {
-	selectedSet := make(map[string]bool)
-	for _, name := range pluginNames {
-		selectedSet[name] = true
-	}
-
-	for plugin, paths := range pluginOwnedPaths {
-		if selectedSet[plugin] {
-			continue
-		}
-		for _, p := range paths {
-			target := filepath.Join(projectDir, p)
-			if err := os.RemoveAll(target); err != nil && !os.IsNotExist(err) {
-				return err
-			}
-		}
-	}
-
-	return nil
-}
-
 // renameFiles maps source file names to destination names (for files that can't use special chars).
 var renameFiles = map[string]string{
 	"_gitignore":  ".gitignore",
diff --git a/libs/apps/initializer/nodejs.go b/libs/apps/initializer/nodejs.go
index 1e96f43f72..b30db46caa 100644
--- a/libs/apps/initializer/nodejs.go
+++ b/libs/apps/initializer/nodejs.go
@@ -40,6 +40,9 @@ func (i *InitializerNodeJs) Initialize(ctx context.Context, workDir string) *Ini
 		}
 	}
 
+	// Step 3: Run postinit script if defined (fully optional — errors are logged, not fatal)
+	i.runNpmPostInit(ctx, workDir)
+
 	return &InitResult{
 		Success: true,
 		Message: "Node.js project initialized successfully",
@@ -102,6 +105,43 @@ func (i *InitializerNodeJs) runAppkitSetup(ctx context.Context, workDir string)
 	})
 }
 
+// runNpmPostInit runs "npm run postinit" if the script is defined in package.json.
+// Failures are logged as warnings and never propagate — postinit is fully optional.
+func (i *InitializerNodeJs) runNpmPostInit(ctx context.Context, workDir string) {
+	if !i.hasNpmScript(workDir, "postinit") {
+		return
+	}
+	err := prompt.RunWithSpinnerCtx(ctx, "Running post-init...", func() error {
+		cmd := exec.CommandContext(ctx, "npm", "run", "postinit")
+		cmd.Dir = workDir
+		cmd.Stdout = nil
+		cmd.Stderr = nil
+		return cmd.Run()
+	})
+	if err != nil {
+		log.Debugf(ctx, "postinit script failed (non-fatal): %v", err)
+	}
+}
+
+// hasNpmScript reports whether the given script name is defined in the project's package.json.
+func (i *InitializerNodeJs) hasNpmScript(workDir, script string) bool {
+	packageJSONPath := filepath.Join(workDir, "package.json")
+	data, err := os.ReadFile(packageJSONPath)
+	if err != nil {
+		return false
+	}
+
+	var pkg struct {
+		Scripts map[string]string `json:"scripts"`
+	}
+	if err := json.Unmarshal(data, &pkg); err != nil {
+		return false
+	}
+
+	_, ok := pkg.Scripts[script]
+	return ok
+}
+
 // hasAppkit checks if the project has @databricks/appkit in its dependencies.
 func (i *InitializerNodeJs) hasAppkit(workDir string) bool {
 	packageJSONPath := filepath.Join(workDir, "package.json")
diff --git a/libs/apps/initializer/nodejs_test.go b/libs/apps/initializer/nodejs_test.go
index eb9095453f..c390517b76 100644
--- a/libs/apps/initializer/nodejs_test.go
+++ b/libs/apps/initializer/nodejs_test.go
@@ -65,3 +65,60 @@ func TestHasAppkitNoPackageJSON(t *testing.T) {
 	init := &InitializerNodeJs{}
 	assert.False(t, init.hasAppkit(tmpDir))
 }
+
+func TestHasNpmScript(t *testing.T) {
+	tests := []struct {
+		name        string
+		packageJSON string
+		script      string
+		want        bool
+	}{
+		{
+			name:        "script present",
+			packageJSON: `{"scripts": {"postinit": "appkit postinit"}}`,
+			script:      "postinit",
+			want:        true,
+		},
+		{
+			name:        "script absent",
+			packageJSON: `{"scripts": {"build": "tsc"}}`,
+			script:      "postinit",
+			want:        false,
+		},
+		{
+			name:        "no scripts section",
+			packageJSON: `{}`,
+			script:      "postinit",
+			want:        false,
+		},
+		{
+			name:        "invalid json",
+			packageJSON: `not json`,
+			script:      "postinit",
+			want:        false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			tmpDir, err := os.MkdirTemp("", "nodejs-test-*")
+			require.NoError(t, err)
+			defer os.RemoveAll(tmpDir)
+
+			err = os.WriteFile(filepath.Join(tmpDir, "package.json"), []byte(tt.packageJSON), 0o644)
+			require.NoError(t, err)
+
+			i := &InitializerNodeJs{}
+			assert.Equal(t, tt.want, i.hasNpmScript(tmpDir, tt.script))
+		})
+	}
+}
+
+func TestHasNpmScriptNoPackageJSON(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "nodejs-test-*")
+	require.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	i := &InitializerNodeJs{}
+	assert.False(t, i.hasNpmScript(tmpDir, "postinit"))
+}