diff --git a/internal/cmd/molecule_step.go b/internal/cmd/molecule_step.go
index d494b91a..f7408bd3 100644
--- a/internal/cmd/molecule_step.go
+++ b/internal/cmd/molecule_step.go
@@ -322,6 +322,12 @@ func handleStepContinue(cwd, townRoot, _ string, nextStep *beads.Issue, dryRun b
 
 	t := tmux.NewTmux()
 
+	// Kill all processes in the pane before respawning to prevent process leaks
+	if err := t.KillPaneProcesses(pane); err != nil {
+		// Non-fatal but log the warning
+		style.PrintWarning("could not kill pane processes: %v", err)
+	}
+
 	// Clear history before respawn
 	if err := t.ClearHistory(pane); err != nil {
 		// Non-fatal
diff --git a/internal/tmux/tmux.go b/internal/tmux/tmux.go
index 8e5f6a49..4b4e6b1b 100644
--- a/internal/tmux/tmux.go
+++ b/internal/tmux/tmux.go
@@ -284,6 +284,48 @@ func getAllDescendants(pid string) []string {
 	return result
 }
 
+// KillPaneProcesses explicitly kills all processes associated with a tmux pane.
+// This prevents orphan processes that survive pane respawn due to SIGHUP being ignored.
+//
+// Process:
+// 1. Get the pane's main process PID
+// 2. Find all descendant processes recursively (not just direct children)
+// 3. Send SIGTERM to all descendants (deepest first)
+// 4. Wait 100ms for graceful shutdown
+// 5. Send SIGKILL to any remaining descendants
+//
+// This ensures Claude processes and all their children are properly terminated
+// before respawning the pane.
+func (t *Tmux) KillPaneProcesses(pane string) error {
+	// Get the pane PID
+	pid, err := t.GetPanePID(pane)
+	if err != nil {
+		return fmt.Errorf("getting pane PID: %w", err)
+	}
+
+	if pid == "" {
+		return fmt.Errorf("pane PID is empty")
+	}
+
+	// Get all descendant PIDs recursively (returns deepest-first order)
+	descendants := getAllDescendants(pid)
+
+	// Send SIGTERM to all descendants (deepest first to avoid orphaning)
+	for _, dpid := range descendants {
+		_ = exec.Command("kill", "-TERM", dpid).Run()
+	}
+
+	// Wait for graceful shutdown
+	time.Sleep(100 * time.Millisecond)
+
+	// Send SIGKILL to any remaining descendants
+	for _, dpid := range descendants {
+		_ = exec.Command("kill", "-KILL", dpid).Run()
+	}
+
+	return nil
+}
+
 // KillServer terminates the entire tmux server and all sessions.
 func (t *Tmux) KillServer() error {
 	_, err := t.run("kill-server")