diff --git a/packages/agent-runtime/src/__tests__/prompts-schema-handling.test.ts b/packages/agent-runtime/src/__tests__/prompts-schema-handling.test.ts
index d3ad20b276..89c5a5f3b2 100644
--- a/packages/agent-runtime/src/__tests__/prompts-schema-handling.test.ts
+++ b/packages/agent-runtime/src/__tests__/prompts-schema-handling.test.ts
@@ -248,6 +248,39 @@ describe('Schema handling error recovery', () => {
       expect(toolSet['problematic_tool']).toBeDefined()
     })
 
+    test('getToolSet keeps an MCP tool schema usable after copying the definition', async () => {
+      // MCP tools arrive as Zod schemas: mcp.ts converts the server's JSON
+      // Schema with convertJsonSchemaToZod. Building the tool set copies the
+      // definition, and lodash drops Zod's non-enumerable `_zod`, which left a
+      // clone that still looked like a schema but threw on any Zod call.
+      const mcpToolDefs = {
+        exa__web_search_exa: {
+          description: 'Search the web with Exa',
+          inputSchema: convertJsonSchemaToZod({
+            type: 'object',
+            properties: { query: { type: 'string' } },
+            required: ['query'],
+          }),
+          endsAgentStep: true,
+        },
+      }
+
+      const toolSet = await getToolSet({
+        toolNames: [],
+        windowedFileReads: false,
+        additionalToolDefinitions: async () => mcpToolDefs,
+        agentTools: {},
+        skills: {},
+      })
+
+      const tool = toolSet['exa__web_search_exa'] as {
+        inputSchema: { safeParse: (input: unknown) => { success: boolean } }
+      }
+      expect(tool).toBeDefined()
+      // A clone without `_zod` throws here instead of validating.
+      expect(tool.inputSchema.safeParse({ query: 'hello' }).success).toBe(true)
+    })
+
     test('ensureZodSchema converts JSON Schema to Zod schema', () => {
       const jsonSchema = {
         type: 'object',
diff --git a/packages/agent-runtime/src/tools/prompts.ts b/packages/agent-runtime/src/tools/prompts.ts
index d3d9110665..d0c7c8a741 100644
--- a/packages/agent-runtime/src/tools/prompts.ts
+++ b/packages/agent-runtime/src/tools/prompts.ts
@@ -430,10 +430,19 @@ export async function getToolSet(params: {
 
   const toolDefinitions = await additionalToolDefinitions()
   for (const [toolName, toolDefinition] of Object.entries(toolDefinitions)) {
-    const clonedDef = cloneDeep(toolDefinition)
+    // Copy the definition without deep-cloning its inputSchema. lodash copies
+    // own *enumerable* properties only, and zod keeps its internals on a
+    // non-enumerable `_zod`, so a deep clone hands back something that still
+    // looks like a schema (`safeParse` lives on the prototype) but has lost
+    // `_zod` -- and the next zod call on it throws "undefined is not an object
+    // (evaluating 'schema._zod.parent')". Every MCP tool hits this, because
+    // mcp.ts stores its input schema as a zod schema. Schemas are immutable, so
+    // carry the reference instead.
+    const { inputSchema, ...restOfDefinition } = toolDefinition
+    const clonedDef = { ...cloneDeep(restOfDefinition), inputSchema }
     // Custom tool inputSchema may be JSON Schema (from SDK) or Zod (from MCP)
     // Ensure it's a Zod schema for the AI SDK
-    const zodSchema = ensureZodSchema(clonedDef.inputSchema)
+    const zodSchema = ensureZodSchema(inputSchema)
     const safeSchema = ensureJsonSchemaCompatible(zodSchema)
     toolSet[toolName] = {
       ...clonedDef,