diff --git a/src/utils/deploy/hash-fns.ts b/src/utils/deploy/hash-fns.ts
index c9edc6379a3..44aae22c14b 100644
--- a/src/utils/deploy/hash-fns.ts
+++ b/src/utils/deploy/hash-fns.ts
@@ -153,6 +153,18 @@ const hashFns = async (
     statusCb,
     tmpDir,
   })
+
+  // ZISI's in-memory FunctionResult only nests bootstrap/runtime version into
+  // buildData when writing the manifest cache. Reconstruct it for direct-zip paths.
+  for (const func of functionZips) {
+    if (!func.buildData) {
+      func.buildData = {
+        bootstrapVersion: func.bootstrapVersion,
+        runtimeAPIVersion: func.runtimeAPIVersion,
+      }
+    }
+  }
+
   const fileObjs = functionZips.map(
     ({
       buildData,
diff --git a/tests/unit/utils/deploy/hash-fns.test.ts b/tests/unit/utils/deploy/hash-fns.test.ts
index d58a5bea0e3..7b10c21c640 100644
--- a/tests/unit/utils/deploy/hash-fns.test.ts
+++ b/tests/unit/utils/deploy/hash-fns.test.ts
@@ -46,3 +46,31 @@ test('Hashes files in a folder', async (t) => {
     })
   })
 })
+
+test('Populates build_data.bootstrapVersion for v2 functions on direct-zip path', async (t) => {
+  await withSiteBuilder(t, async (builder) => {
+    await builder
+      .withNetlifyToml({ config: { functions: { directory: 'functions' } } })
+      .withFunction({
+        path: 'hello.js',
+        runtimeAPIVersion: 2,
+        handler: (_req: Request) => new Response('Hello'),
+      })
+      .build()
+
+    const { fnConfig } = await hashFns(new BaseCommand(), [path.join(builder.directory, 'functions')], {
+      tmpDir: temporaryDirectory(),
+      concurrentHash: DEFAULT_CONCURRENT_HASH,
+      statusCb() {},
+    })
+
+    expect(fnConfig).toBeDefined()
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion -- covered by expectation above
+    const helloConfig = fnConfig!.hello as { build_data?: { bootstrapVersion?: string; runtimeAPIVersion?: number } }
+    expect(helloConfig).toBeDefined()
+    expect(helloConfig.build_data).toBeDefined()
+    expect(helloConfig.build_data?.runtimeAPIVersion).toBe(2)
+    expect(helloConfig.build_data?.bootstrapVersion).toEqual(expect.any(String))
+    expect(helloConfig.build_data?.bootstrapVersion).not.toBe('')
+  })
+})