diff --git a/pkg/mcp/mcp.go b/pkg/mcp/mcp.go
index ccdf1ae..56694d6 100644
--- a/pkg/mcp/mcp.go
+++ b/pkg/mcp/mcp.go
@@ -8,6 +8,7 @@ import (
 	"context"
 	"iter"
 	"net/http"
+	"os"
 	"slices"
 	"sync"
 
@@ -661,7 +662,10 @@ func (s *Service) Run(ctx context.Context) error {
 		return s.ServeTCP(ctx, addr)
 	}
 	s.stdioMode = true
-	return s.server.Run(ctx, &mcp.StdioTransport{})
+	return s.server.Run(ctx, &mcp.IOTransport{
+		Reader: os.Stdin,
+		Writer: sharedStdout,
+	})
 }
 
 
diff --git a/pkg/mcp/notify.go b/pkg/mcp/notify.go
index 34b91c4..774e1db 100644
--- a/pkg/mcp/notify.go
+++ b/pkg/mcp/notify.go
@@ -8,6 +8,7 @@ package mcp
 
 import (
 	"context"
+	"io"
 	"iter"
 	"os"
 	"sync"
@@ -16,8 +17,25 @@ import (
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 )
 
-// stdoutMu protects stdout writes from concurrent goroutines.
-var stdoutMu sync.Mutex
+// lockedWriter wraps an io.Writer with a mutex.
+// Both the SDK's transport and ChannelSend use this writer,
+// ensuring channel notifications don't interleave with SDK messages.
+type lockedWriter struct {
+	mu sync.Mutex
+	w  io.Writer
+}
+
+func (lw *lockedWriter) Write(p []byte) (int, error) {
+	lw.mu.Lock()
+	defer lw.mu.Unlock()
+	return lw.w.Write(p)
+}
+
+func (lw *lockedWriter) Close() error { return nil }
+
+// sharedStdout is the single writer for all stdio output.
+// Created once when the MCP service enters stdio mode.
+var sharedStdout = &lockedWriter{w: os.Stdout}
 
 // SendNotificationToAllClients broadcasts a log-level notification to every
 // connected MCP session (stdio, HTTP, TCP, and Unix).
@@ -71,16 +89,12 @@ func (s *Service) ChannelSend(ctx context.Context, channel string, data any) {
 
 	msg := core.JSONMarshalString(notification)
 
-	// Write directly to stdout (stdio transport) with newline delimiter.
-	// The official SDK doesn't expose a way to send custom notification methods,
-	// so we write the JSON-RPC notification directly to the transport.
-	// Only write when running in stdio mode — HTTP/TCP transports don't use stdout.
+	// Write through the shared locked writer (same one the SDK transport uses).
+	// This prevents channel notifications from interleaving with SDK messages.
 	if !s.stdioMode {
 		return
 	}
-	stdoutMu.Lock()
-	os.Stdout.Write([]byte(core.Concat(msg, "\n")))
-	stdoutMu.Unlock()
+	sharedStdout.Write([]byte(core.Concat(msg, "\n")))
 }
 
 // ChannelSendToSession pushes a channel event to a specific session.