diff --git a/src/shared/protocol-transport-handling.test.ts b/src/shared/protocol-transport-handling.test.ts
new file mode 100644
index 000000000..3baa9b638
--- /dev/null
+++ b/src/shared/protocol-transport-handling.test.ts
@@ -0,0 +1,189 @@
+import { describe, expect, test, beforeEach } from "@jest/globals";
+import { Protocol } from "./protocol.js";
+import { Transport } from "./transport.js";
+import { Request, Notification, Result, JSONRPCMessage } from "../types.js";
+import { z } from "zod";
+
+// Mock Transport class
+class MockTransport implements Transport {
+  id: string;
+  onclose?: () => void;
+  onerror?: (error: Error) => void;
+  onmessage?: (message: unknown) => void;
+  sentMessages: JSONRPCMessage[] = [];
+
+  constructor(id: string) {
+    this.id = id;
+  }
+
+  async start(): Promise<void> {}
+  
+  async close(): Promise<void> {
+    this.onclose?.();
+  }
+  
+  async send(message: JSONRPCMessage): Promise<void> {
+    this.sentMessages.push(message);
+  }
+}
+
+describe("Protocol transport handling bug", () => {
+  let protocol: Protocol<Request, Notification, Result>;
+  let transportA: MockTransport;
+  let transportB: MockTransport;
+
+  beforeEach(() => {
+    protocol = new (class extends Protocol<Request, Notification, Result> {
+      protected assertCapabilityForMethod(): void {}
+      protected assertNotificationCapability(): void {}
+      protected assertRequestHandlerCapability(): void {}
+    })();
+    
+    transportA = new MockTransport("A");
+    transportB = new MockTransport("B");
+  });
+
+  test("should send response to the correct transport when multiple clients are connected", async () => {
+    // Set up a request handler that simulates processing time
+    let resolveHandler: (value: Result) => void;
+    const handlerPromise = new Promise<Result>((resolve) => {
+      resolveHandler = resolve;
+    });
+
+    const TestRequestSchema = z.object({
+      method: z.literal("test/method"),
+      params: z.object({
+        from: z.string()
+      }).optional()
+    });
+
+    protocol.setRequestHandler(
+      TestRequestSchema,
+      async (request) => {
+        console.log(`Processing request from ${request.params?.from}`);
+        return handlerPromise;
+      }
+    );
+
+    // Client A connects and sends a request
+    await protocol.connect(transportA);
+    
+    const requestFromA = {
+      jsonrpc: "2.0" as const,
+      method: "test/method",
+      params: { from: "clientA" },
+      id: 1
+    };
+    
+    // Simulate client A sending a request
+    transportA.onmessage?.(requestFromA);
+    
+    // While A's request is being processed, client B connects
+    // This overwrites the transport reference in the protocol
+    await protocol.connect(transportB);
+    
+    const requestFromB = {
+      jsonrpc: "2.0" as const,
+      method: "test/method", 
+      params: { from: "clientB" },
+      id: 2
+    };
+    
+    // Client B sends its own request
+    transportB.onmessage?.(requestFromB);
+    
+    // Now complete A's request
+    resolveHandler!({ data: "responseForA" } as Result);
+    
+    // Wait for async operations to complete
+    await new Promise(resolve => setTimeout(resolve, 10));
+    
+    // Check where the responses went
+    console.log("Transport A received:", transportA.sentMessages);
+    console.log("Transport B received:", transportB.sentMessages);
+    
+    // FIXED: Each transport now receives its own response
+    
+    // Transport A should receive response for request ID 1
+    expect(transportA.sentMessages.length).toBe(1);
+    expect(transportA.sentMessages[0]).toMatchObject({
+      jsonrpc: "2.0",
+      id: 1,
+      result: { data: "responseForA" }
+    });
+    
+    // Transport B should only receive its own response (when implemented)
+    expect(transportB.sentMessages.length).toBe(1);
+    expect(transportB.sentMessages[0]).toMatchObject({
+      jsonrpc: "2.0",
+      id: 2,
+      result: { data: "responseForA" } // Same handler result in this test
+    });
+  });
+
+  test("demonstrates the timing issue with multiple rapid connections", async () => {
+    const delays: number[] = [];
+    const results: { transport: string; response: JSONRPCMessage[] }[] = [];
+    
+    const DelayedRequestSchema = z.object({
+      method: z.literal("test/delayed"),
+      params: z.object({
+        delay: z.number(),
+        client: z.string()
+      }).optional()
+    });
+
+    // Set up handler with variable delay
+    protocol.setRequestHandler(
+      DelayedRequestSchema,
+      async (request, extra) => {
+        const delay = request.params?.delay || 0;
+        delays.push(delay);
+        
+        await new Promise(resolve => setTimeout(resolve, delay));
+        
+        return { 
+          processedBy: `handler-${extra.requestId}`,
+          delay: delay
+        } as Result;
+      }
+    );
+
+    // Rapid succession of connections and requests
+    await protocol.connect(transportA);
+    transportA.onmessage?.({
+      jsonrpc: "2.0" as const,
+      method: "test/delayed",
+      params: { delay: 50, client: "A" },
+      id: 1
+    });
+
+    // Connect B while A is processing
+    setTimeout(async () => {
+      await protocol.connect(transportB);
+      transportB.onmessage?.({
+        jsonrpc: "2.0" as const,
+        method: "test/delayed", 
+        params: { delay: 10, client: "B" },
+        id: 2
+      });
+    }, 10);
+
+    // Wait for all processing
+    await new Promise(resolve => setTimeout(resolve, 100));
+
+    // Collect results
+    if (transportA.sentMessages.length > 0) {
+      results.push({ transport: "A", response: transportA.sentMessages });
+    }
+    if (transportB.sentMessages.length > 0) {
+      results.push({ transport: "B", response: transportB.sentMessages });
+    }
+
+    console.log("Timing test results:", results);
+    
+    // FIXED: Each transport receives its own responses
+    expect(transportA.sentMessages.length).toBe(1);
+    expect(transportB.sentMessages.length).toBe(1);
+  });
+});
\ No newline at end of file
diff --git a/src/shared/protocol.ts b/src/shared/protocol.ts
index 6142140dd..90173f2fc 100644
--- a/src/shared/protocol.ts
+++ b/src/shared/protocol.ts
@@ -367,8 +367,11 @@ export abstract class Protocol<
     const handler =
       this._requestHandlers.get(request.method) ?? this.fallbackRequestHandler;
 
+    // Capture the current transport at request time to ensure responses go to the correct client
+    const capturedTransport = this._transport;
+
     if (handler === undefined) {
-      this._transport
+      capturedTransport
         ?.send({
           jsonrpc: "2.0",
           id: request.id,
@@ -390,7 +393,7 @@ export abstract class Protocol<
 
     const fullExtra: RequestHandlerExtra<SendRequestT, SendNotificationT> = {
       signal: abortController.signal,
-      sessionId: this._transport?.sessionId,
+      sessionId: capturedTransport?.sessionId,
       _meta: request.params?._meta,
       sendNotification:
         (notification) =>
@@ -411,7 +414,7 @@ export abstract class Protocol<
             return;
           }
 
-          return this._transport?.send({
+          return capturedTransport?.send({
             result,
             jsonrpc: "2.0",
             id: request.id,
@@ -422,7 +425,7 @@ export abstract class Protocol<
             return;
           }
 
-          return this._transport?.send({
+          return capturedTransport?.send({
             jsonrpc: "2.0",
             id: request.id,
             error: {