diff --git a/pkg/agent/core.go b/pkg/agent/core.go
index ce36572..22407c2 100644
--- a/pkg/agent/core.go
+++ b/pkg/agent/core.go
@@ -180,6 +180,7 @@ type agent struct {
 	env             map[string]string // session-scoped env vars
 	changeMu        sync.Mutex
 	changeCond      *sync.Cond
+	submitMu        sync.Mutex // serializes Submit calls (commands + turns)
 }
 
 // SetEnv stores a session-scoped variable and propagates it to the execute server.
@@ -673,6 +674,23 @@ func (s *agent) Submit(ctx context.Context, input string, handler EventHandler)
 	if input == "" {
 		return
 	}
+
+	// Fast path: inject and FIFO push use atomics and are safe without
+	// the submit lock. Handle them before acquiring submitMu so they
+	// don't block behind a long-running turn or command.
+	if s.IsRunning() {
+		if s.handleCommand(ctx, input, handler) {
+			return
+		}
+		s.fifo.Push(input)
+		return
+	}
+
+	// Serialize commands and turns so that e.g. a /compact arriving via
+	// ctl cannot race with an executeTurn arriving via prompt.
+	s.submitMu.Lock()
+	defer s.submitMu.Unlock()
+
 	if s.handleCommand(ctx, input, handler) {
 		return
 	}
diff --git a/pkg/store/store_test.go b/pkg/store/store_test.go
index 63bf30a..9444cfe 100644
--- a/pkg/store/store_test.go
+++ b/pkg/store/store_test.go
@@ -41,6 +41,7 @@ type stubCore struct {
 	queued     []string
 	interrupted     bool
 	setSessionIDErr error
+	submitCh        chan struct{} // closed after each Submit call
 }
 
 func (c *stubCore) Submit(_ context.Context, input string, handler agent.EventHandler) {
@@ -48,6 +49,9 @@ func (c *stubCore) Submit(_ context.Context, input string, handler agent.EventHa
 	if handler != nil && c.reply != "" {
 		handler(agent.Event{Role: "assistant", Content: c.reply})
 	}
+	if c.submitCh != nil {
+		close(c.submitCh)
+	}
 }
 func (c *stubCore) Interrupt(error) bool                                        { c.interrupted = true; return c.running }
 func (c *stubCore) Inject(string)                                               {}
@@ -815,8 +819,9 @@ func TestSessionFileStoreWritePrompt(t *testing.T) {
 	defer sess.Cancel()
 	sf, core := newSessionFileStore(t, sess)
 
+	core.submitCh = make(chan struct{})
 	storeWrite(t, sf, "prompt", []byte("hello agent"))
-	time.Sleep(10 * time.Millisecond)
+	<-core.submitCh
 	if len(core.submitted) != 1 || core.submitted[0] != "hello agent" {
 		t.Errorf("submitted = %v; want [hello agent]", core.submitted)
 	}