diff --git a/.changeset/clean-brooms-travel.md b/.changeset/clean-brooms-travel.md
new file mode 100644
index 0000000000..f56cf1e467
--- /dev/null
+++ b/.changeset/clean-brooms-travel.md
@@ -0,0 +1,5 @@
+---
+"@workflow/nitro": patch
+---
+
+Pass configured Nitro workflow scan directories through to Workflow builders.
diff --git a/packages/nitro/src/builders.ts b/packages/nitro/src/builders.ts
index 7a8e91f41f..8667feb574 100644
--- a/packages/nitro/src/builders.ts
+++ b/packages/nitro/src/builders.ts
@@ -31,13 +31,17 @@ function getNitroProjectRoot(nitro: Nitro): string {
   return nitro.options.workspaceDir ?? nitro.options.rootDir;
 }
 
+function getNitroWorkflowDirs(nitro: Nitro): string[] {
+  return nitro.options.workflow?.dirs ?? ['.'];
+}
+
 export class VercelBuilder extends VercelBuildOutputAPIBuilder {
   constructor(nitro: Nitro) {
     super({
       ...createBaseBuilderConfig({
         workingDir: nitro.options.rootDir,
         projectRoot: getNitroProjectRoot(nitro),
-        dirs: ['.'], // Different apps that use nitro have different directories
+        dirs: getNitroWorkflowDirs(nitro),
         runtime: nitro.options.workflow?.runtime,
         sourcemap: nitro.options.workflow?.sourcemap,
         externalPackages: getNitroStringExternals(nitro),
@@ -67,7 +71,7 @@ export class LocalBuilder extends BaseBuilder {
         workingDir: nitro.options.rootDir,
         projectRoot: getNitroProjectRoot(nitro),
         watch: nitro.options.dev,
-        dirs: ['.'], // Different apps that use nitro have different directories
+        dirs: getNitroWorkflowDirs(nitro),
         sourcemap: nitro.options.workflow?.sourcemap,
         externalPackages: getNitroStringExternals(nitro),
       }),
diff --git a/packages/nitro/src/index.test.ts b/packages/nitro/src/index.test.ts
index 1b0e95bb55..d32dfd83c1 100644
--- a/packages/nitro/src/index.test.ts
+++ b/packages/nitro/src/index.test.ts
@@ -9,7 +9,7 @@ type StubOptions = {
   dev?: boolean;
   preset?: string;
   workspaceDir?: string;
-  workflow?: { runtime?: string };
+  workflow?: { dirs?: string[]; runtime?: string };
   externals?: {
     external?: Array<string | RegExp | ((id: string) => boolean)>;
   };
@@ -332,6 +332,18 @@ describe('@workflow/nitro externals forwarding', () => {
         expect(builder.config.projectRoot).toBe('/tmp');
       });
 
+      it('forwards workflow.dirs to the workflow builder', () => {
+        const nitro = createNitroStub({
+          routing: true,
+          workflow: { dirs: ['server/workflows', 'layers/custom/workflows'] },
+        });
+        const builder = new Builder(nitro) as any;
+        expect(builder.config.dirs).toEqual([
+          'server/workflows',
+          'layers/custom/workflows',
+        ]);
+      });
+
       it('forwards string entries from nitro.options.externals.external', () => {
         const nitro = createNitroStub({
           routing: true,