diff --git a/internal/refinery/manager.go b/internal/refinery/manager.go
index 980926e6..66e48c80 100644
--- a/internal/refinery/manager.go
+++ b/internal/refinery/manager.go
@@ -744,9 +744,16 @@ func (m *Manager) RejectMR(idOrBranch string, reason string, notify bool) (*Merg
 		return nil, fmt.Errorf("%w: MR is already closed with reason: %s", ErrClosedImmutable, mr.CloseReason)
 	}
 
-	// Close with rejected reason
+	// Close the bead in storage with the rejection reason
+	b := beads.New(m.rig.BeadsPath())
+	if err := b.CloseWithReason("rejected: "+reason, mr.ID); err != nil {
+		return nil, fmt.Errorf("failed to close MR bead: %w", err)
+	}
+
+	// Update in-memory state for return value
 	if err := mr.Close(CloseReasonRejected); err != nil {
-		return nil, fmt.Errorf("failed to close MR: %w", err)
+		// Non-fatal: bead is already closed, just log
+		_, _ = fmt.Fprintf(m.output, "Warning: failed to update MR state: %v\n", err)
 	}
 	mr.Error = reason