diff --git a/src/agents/pi-embedded-runner.ts b/src/agents/pi-embedded-runner.ts
index f8acdd185..83678ac4e 100644
--- a/src/agents/pi-embedded-runner.ts
+++ b/src/agents/pi-embedded-runner.ts
@@ -1313,6 +1313,8 @@ export async function runEmbeddedPiAgent(params: {
     mediaUrls?: string[];
     audioAsVoice?: boolean;
   }) => void | Promise<void>;
+  /** Flush pending block replies (e.g., before tool execution to preserve message boundaries). */
+  onBlockReplyFlush?: () => void | Promise<void>;
   blockReplyBreak?: "text_end" | "message_end";
   blockReplyChunking?: BlockReplyChunking;
   onReasoningStream?: (payload: {
@@ -1669,6 +1671,7 @@ export async function runEmbeddedPiAgent(params: {
               onToolResult: params.onToolResult,
               onReasoningStream: params.onReasoningStream,
               onBlockReply: params.onBlockReply,
+              onBlockReplyFlush: params.onBlockReplyFlush,
               blockReplyBreak: params.blockReplyBreak,
               blockReplyChunking: params.blockReplyChunking,
               onPartialReply: params.onPartialReply,
diff --git a/src/agents/pi-embedded-subscribe.test.ts b/src/agents/pi-embedded-subscribe.test.ts
index d07691e90..974faea4d 100644
--- a/src/agents/pi-embedded-subscribe.test.ts
+++ b/src/agents/pi-embedded-subscribe.test.ts
@@ -1754,4 +1754,96 @@ describe("subscribeEmbeddedPiSession", () => {
 
     expect(onToolResult).toHaveBeenCalledTimes(1);
   });
+
+  it("calls onBlockReplyFlush before tool_execution_start to preserve message boundaries", () => {
+    let handler: SessionEventHandler | undefined;
+    const session: StubSession = {
+      subscribe: (fn) => {
+        handler = fn;
+        return () => {};
+      },
+    };
+
+    const onBlockReplyFlush = vi.fn();
+    const onBlockReply = vi.fn();
+
+    subscribeEmbeddedPiSession({
+      session: session as unknown as Parameters<
+        typeof subscribeEmbeddedPiSession
+      >[0]["session"],
+      runId: "run-flush-test",
+      onBlockReply,
+      onBlockReplyFlush,
+      blockReplyBreak: "text_end",
+    });
+
+    // Simulate text arriving before tool
+    handler?.({
+      type: "message_start",
+      message: { role: "assistant" },
+    });
+
+    handler?.({
+      type: "message_update",
+      message: { role: "assistant" },
+      assistantMessageEvent: {
+        type: "text_delta",
+        delta: "First message before tool.",
+      },
+    });
+
+    expect(onBlockReplyFlush).not.toHaveBeenCalled();
+
+    // Tool execution starts - should trigger flush
+    handler?.({
+      type: "tool_execution_start",
+      toolName: "bash",
+      toolCallId: "tool-flush-1",
+      args: { command: "echo hello" },
+    });
+
+    expect(onBlockReplyFlush).toHaveBeenCalledTimes(1);
+
+    // Another tool - should flush again
+    handler?.({
+      type: "tool_execution_start",
+      toolName: "read",
+      toolCallId: "tool-flush-2",
+      args: { path: "/tmp/test.txt" },
+    });
+
+    expect(onBlockReplyFlush).toHaveBeenCalledTimes(2);
+  });
+
+  it("does not call onBlockReplyFlush when callback is not provided", () => {
+    let handler: SessionEventHandler | undefined;
+    const session: StubSession = {
+      subscribe: (fn) => {
+        handler = fn;
+        return () => {};
+      },
+    };
+
+    const onBlockReply = vi.fn();
+
+    // No onBlockReplyFlush provided
+    subscribeEmbeddedPiSession({
+      session: session as unknown as Parameters<
+        typeof subscribeEmbeddedPiSession
+      >[0]["session"],
+      runId: "run-no-flush",
+      onBlockReply,
+      blockReplyBreak: "text_end",
+    });
+
+    // This should not throw even without onBlockReplyFlush
+    expect(() => {
+      handler?.({
+        type: "tool_execution_start",
+        toolName: "bash",
+        toolCallId: "tool-no-flush",
+        args: { command: "echo test" },
+      });
+    }).not.toThrow();
+  });
 });
diff --git a/src/agents/pi-embedded-subscribe.ts b/src/agents/pi-embedded-subscribe.ts
index 9d3d325e9..f69209dd0 100644
--- a/src/agents/pi-embedded-subscribe.ts
+++ b/src/agents/pi-embedded-subscribe.ts
@@ -198,6 +198,8 @@ export function subscribeEmbeddedPiSession(params: {
     mediaUrls?: string[];
     audioAsVoice?: boolean;
   }) => void | Promise<void>;
+  /** Flush pending block replies (e.g., before tool execution to preserve message boundaries). */
+  onBlockReplyFlush?: () => void | Promise<void>;
   blockReplyBreak?: "text_end" | "message_end";
   blockReplyChunking?: BlockReplyChunking;
   onPartialReply?: (payload: {
@@ -483,6 +485,11 @@ export function subscribeEmbeddedPiSession(params: {
       }
 
       if (evt.type === "tool_execution_start") {
+        // Flush pending block replies to preserve message boundaries before tool execution
+        if (params.onBlockReplyFlush) {
+          void params.onBlockReplyFlush();
+        }
+
         const toolName = String(
           (evt as AgentEvent & { toolName: string }).toolName,
         );
diff --git a/src/auto-reply/reply/agent-runner.ts b/src/auto-reply/reply/agent-runner.ts
index 6b3229286..23f7f8986 100644
--- a/src/auto-reply/reply/agent-runner.ts
+++ b/src/auto-reply/reply/agent-runner.ts
@@ -643,6 +643,12 @@ export async function runReplyAgent(params: {
                       blockReplyPipeline?.enqueue(blockPayload);
                     }
                   : undefined,
+              onBlockReplyFlush:
+                blockStreamingEnabled && blockReplyPipeline
+                  ? async () => {
+                      await blockReplyPipeline.flush({ force: true });
+                    }
+                  : undefined,
               shouldEmitToolResult,
               onToolResult: opts?.onToolResult
                 ? (payload) => {