diff --git a/packages/core/src/permission.ts b/packages/core/src/permission.ts
index acc0705352c1..763d5e583587 100644
--- a/packages/core/src/permission.ts
+++ b/packages/core/src/permission.ts
@@ -183,6 +183,12 @@ const layer = Layer.effect(
       return { effect: event.effect, message: event.message, rules: all }
     })
 
+    // Metadata is JSON-encoded; drop undefined values tools pass for absent optional inputs.
+    function metadata(value: AssertInput["metadata"]): Request["metadata"] {
+      if (!value) return value
+      return Object.fromEntries(Object.entries(value).filter(([, item]) => item !== undefined))
+    }
+
     function request(input: AssertInput, message?: string): Request {
       return {
         id: input.id ?? ID.create(),
@@ -190,7 +196,7 @@ const layer = Layer.effect(
         action: input.action,
         resources: input.resources,
         save: input.save,
-        metadata: input.metadata,
+        metadata: metadata(input.metadata),
         source: input.source,
         message,
       }
diff --git a/packages/core/test/permission.test.ts b/packages/core/test/permission.test.ts
index 6dba198515b4..30efde2ba588 100644
--- a/packages/core/test/permission.test.ts
+++ b/packages/core/test/permission.test.ts
@@ -260,6 +260,17 @@ describe("Permission", () => {
     }),
   )
 
+  it.effect("omits undefined metadata values from pending requests", () =>
+    Effect.gen(function* () {
+      yield* setup()
+      const service = yield* Permission.Service
+      yield* service.ask(assertion({ metadata: { root: ".", path: undefined, limit: undefined } }))
+      const request = yield* service.get(Permission.ID.create("per_test"))
+      expect(request?.metadata).toEqual({ root: "." })
+      expect(Object.keys(request?.metadata ?? {})).toEqual(["root"])
+    }),
+  )
+
   it.effect("defects when an asked permission is declined", () =>
     Effect.gen(function* () {
       yield* setup()