diff --git a/README.md b/README.md
index 92f56786f..e0bb82ef2 100644
--- a/README.md
+++ b/README.md
@@ -1399,6 +1399,24 @@ This setup allows you to:
 - Provide custom documentation URLs
 - Maintain control over the OAuth flow while delegating to an external provider
 
+### Schema generation compatibility
+
+Some MCP clients doesn't support schemas with $refs very well, specially with large schemas. You can pass options to the McpServer constructor that explicitly request generating an input / output schema with no $ref.
+
+```typescript
+const mcpServer = new McpServer(
+    {
+        name: 'test server',
+        version: '1.0'
+    },
+    {
+        zodToJsonSchemaOptions: {
+            $refStrategy: 'none'
+        }
+    }
+);
+```
+
 ### Backwards Compatibility
 
 Clients and servers with StreamableHttp transport can maintain [backwards compatibility](https://modelcontextprotocol.io/specification/2025-03-26/basic/transports#backwards-compatibility) with the deprecated HTTP+SSE transport (from protocol version 2024-11-05) as follows
diff --git a/src/server/mcp.test.ts b/src/server/mcp.test.ts
index f3669fa64..6ccc0d0f6 100644
--- a/src/server/mcp.test.ts
+++ b/src/server/mcp.test.ts
@@ -1685,6 +1685,141 @@ describe('tool()', () => {
         expect(result.tools[0].name).toBe('test-without-meta');
         expect(result.tools[0]._meta).toBeUndefined();
     });
+
+    /***
+     * Test: Tool Registration with a complex schema containing $refs should keep the $refs by default
+     */
+    test('should register tool with a schema with $refs by default', async () => {
+        const mcpServer = new McpServer({
+            name: 'test server',
+            version: '1.0'
+        });
+        const client = new Client({
+            name: 'test client',
+            version: '1.0'
+        });
+
+        const addressType = z.object({
+            street: z.string(),
+            city: z.string()
+        });
+
+        mcpServer.registerTool(
+            'test-with-complex-schema',
+            {
+                description: 'A tool with a complex schema with refs',
+                inputSchema: {
+                    name: z.string(),
+                    primary_address: addressType,
+                    secondary_address: addressType
+                },
+                outputSchema: {
+                    name: z.string(),
+                    primary_address: addressType,
+                    secondary_address: addressType
+                }
+            },
+            async ({ name }) => ({
+                content: [{ type: 'text', text: `Hello, ${name}!` }]
+            })
+        );
+
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+
+        await Promise.all([client.connect(clientTransport), mcpServer.server.connect(serverTransport)]);
+
+        const result = await client.request({ method: 'tools/list' }, ListToolsResultSchema);
+
+        expect(result.tools).toHaveLength(1);
+        expect(result.tools[0].name).toBe('test-with-complex-schema');
+        expect(result.tools[0].inputSchema).toMatchObject({
+            type: 'object',
+            properties: {
+                name: { type: 'string' },
+                primary_address: { type: 'object', properties: { street: { type: 'string' }, city: { type: 'string' } } },
+                secondary_address: { $ref: '#/properties/primary_address' }
+            }
+        });
+        expect(result.tools[0].outputSchema).toMatchObject({
+            type: 'object',
+            properties: {
+                name: { type: 'string' },
+                primary_address: { type: 'object', properties: { street: { type: 'string' }, city: { type: 'string' } } },
+                secondary_address: { $ref: '#/properties/primary_address' }
+            }
+        });
+    });
+
+    /***
+     * Test: Tool Registration with a complex schema containing $refs should not use $refs when disabled
+     */
+    test('should register tool with a schema with not $refs if configured', async () => {
+        const mcpServer = new McpServer(
+            {
+                name: 'test server',
+                version: '1.0'
+            },
+            {
+                zodToJsonSchemaOptions: {
+                    $refStrategy: 'none'
+                }
+            }
+        );
+        const client = new Client({
+            name: 'test client',
+            version: '1.0'
+        });
+
+        const addressType = z.object({
+            street: z.string(),
+            city: z.string()
+        });
+
+        mcpServer.registerTool(
+            'test-with-complex-schema',
+            {
+                description: 'A tool with a complex schema with refs',
+                inputSchema: {
+                    name: z.string(),
+                    primary_address: addressType,
+                    secondary_address: addressType
+                },
+                outputSchema: {
+                    name: z.string(),
+                    primary_address: addressType,
+                    secondary_address: addressType
+                }
+            },
+            async ({ name }) => ({
+                content: [{ type: 'text', text: `Hello, ${name}!` }]
+            })
+        );
+
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+
+        await Promise.all([client.connect(clientTransport), mcpServer.server.connect(serverTransport)]);
+
+        const result = await client.request({ method: 'tools/list' }, ListToolsResultSchema);
+
+        expect(result.tools).toHaveLength(1);
+        expect(result.tools[0].name).toBe('test-with-complex-schema');
+        expect(result.tools[0].inputSchema).toMatchObject({
+            type: 'object',
+            properties: {
+                name: { type: 'string' },
+                primary_address: { type: 'object', properties: { street: { type: 'string' }, city: { type: 'string' } } },
+                secondary_address: { type: 'object', properties: { street: { type: 'string' }, city: { type: 'string' } } }
+            }
+        });
+        expect(result.tools[0].outputSchema).toMatchObject({
+            type: 'object',
+            properties: {
+                name: { type: 'string' },
+                primary_address: { type: 'object', properties: { street: { type: 'string' }, city: { type: 'string' } } },
+                secondary_address: { type: 'object', properties: { street: { type: 'string' }, city: { type: 'string' } } }
+            }
+        });
+    });
 });
 
 describe('resource()', () => {
diff --git a/src/server/mcp.ts b/src/server/mcp.ts
index 015f518a1..1eafb82c3 100644
--- a/src/server/mcp.ts
+++ b/src/server/mcp.ts
@@ -55,8 +55,10 @@ export class McpServer {
     } = {};
     private _registeredTools: { [name: string]: RegisteredTool } = {};
     private _registeredPrompts: { [name: string]: RegisteredPrompt } = {};
+    private _schemaGenerationOptions: SchemaGenerationOption = {};
 
-    constructor(serverInfo: Implementation, options?: ServerOptions) {
+    constructor(serverInfo: Implementation, options?: ServerOptions & SchemaGenerationOption) {
+        this._schemaGenerationOptions = options || {};
         this.server = new Server(serverInfo, options);
     }
 
@@ -105,7 +107,8 @@ export class McpServer {
                             inputSchema: tool.inputSchema
                                 ? (zodToJsonSchema(tool.inputSchema, {
                                       strictUnions: true,
-                                      pipeStrategy: 'input'
+                                      pipeStrategy: 'input',
+                                      ...(this._schemaGenerationOptions.zodToJsonSchemaOptions ?? {})
                                   }) as Tool['inputSchema'])
                                 : EMPTY_OBJECT_JSON_SCHEMA,
                             annotations: tool.annotations,
@@ -115,7 +118,8 @@ export class McpServer {
                         if (tool.outputSchema) {
                             toolDefinition.outputSchema = zodToJsonSchema(tool.outputSchema, {
                                 strictUnions: true,
-                                pipeStrategy: 'output'
+                                pipeStrategy: 'output',
+                                ...(this._schemaGenerationOptions.zodToJsonSchemaOptions ?? {})
                             }) as Tool['outputSchema'];
                         }
 
@@ -1017,6 +1021,21 @@ export class ResourceTemplate {
     }
 }
 
+/**
+ * Options for schema generation.
+ */
+export type SchemaGenerationOption = {
+    /**
+     * Options for zod-to-json-schema conversion.
+     * Only one field is currently supported: `$refStrategy`, and with two possible values where
+     * the library accepts two others which are not relevant here.
+     * Useful to set to 'none' to avoid $ref generation because some clients do not support them well.
+     */
+    zodToJsonSchemaOptions?: {
+        $refStrategy?: 'root' | 'none';
+    };
+};
+
 /**
  * Callback for a tool handler registered with Server.tool().
  *