diff --git a/pkg/api/handlers/mcpcatalogs.go b/pkg/api/handlers/mcpcatalogs.go
index c2f8f50c1d..958012ac88 100644
--- a/pkg/api/handlers/mcpcatalogs.go
+++ b/pkg/api/handlers/mcpcatalogs.go
@@ -1251,6 +1251,11 @@ func (h *MCPCatalogHandler) RefreshCompositeComponents(req api.Context) error {
 		}
 	}
 
+	// Validate the refreshed manifest to ensure it's still valid
+	if err := validation.ValidateCatalogEntryManifest(entry.Spec.Manifest); err != nil {
+		return types.NewErrBadRequest("failed to validate entry manifest: %v", err)
+	}
+
 	// Update the entry
 	if err := req.Update(&entry); err != nil {
 		return fmt.Errorf("failed to update entry: %w", err)
diff --git a/pkg/storage/apis/obot.obot.ai/v1/mcpserver.go b/pkg/storage/apis/obot.obot.ai/v1/mcpserver.go
index 59119a62f8..f19eefdf27 100644
--- a/pkg/storage/apis/obot.obot.ai/v1/mcpserver.go
+++ b/pkg/storage/apis/obot.obot.ai/v1/mcpserver.go
@@ -63,13 +63,18 @@ func (in *MCPServer) FieldNames() []string {
 }
 
 func (in *MCPServer) DeleteRefs() []Ref {
-	return []Ref{
+	refs := []Ref{
 		{ObjType: &Thread{}, Name: in.Spec.ThreadName},
-		{ObjType: &MCPServerCatalogEntry{}, Name: in.Spec.MCPServerCatalogEntryName},
 		{ObjType: &MCPCatalog{}, Name: in.Spec.MCPCatalogID},
 		{ObjType: &PowerUserWorkspace{}, Name: in.Spec.PowerUserWorkspaceID},
 		{ObjType: &MCPServer{}, Name: in.Spec.CompositeName},
 	}
+	if in.Spec.CompositeName == "" {
+		// Only garbage collect an MCP server when the catalog entry is deleted if it's not a component of a composite MCP server.
+		// Component MCP servers get their manifest from the composite catalog entry instead.
+		refs = append(refs, Ref{ObjType: &MCPServerCatalogEntry{}, Name: in.Spec.MCPServerCatalogEntryName})
+	}
+	return refs
 }
 
 type MCPServerSpec struct {