diff --git a/pkg/topology/component_config.go b/pkg/topology/component_config.go
index 832070261..61ad33d4f 100644
--- a/pkg/topology/component_config.go
+++ b/pkg/topology/component_config.go
@@ -41,6 +41,14 @@ var ComponentConfigRun = &job.Job{
 			}
 			run.History.IncrSuccess()
 		}
+
+		// Cleanup dead relationships
+		componentIDsWithConfigs := lo.Map(components, func(c pkg.Component, _ int) string { return c.ID.String() })
+		if err := db.Table("config_component_relationships").
+			Where("component_id NOT IN ?", componentIDsWithConfigs).
+			Update("deleted_at", duty.Now()).Error; err != nil {
+			return fmt.Errorf("error cleaning up old config_component_relationships: %w", err)
+		}
 		return nil
 	},
 }
diff --git a/pkg/topology/component_relationship.go b/pkg/topology/component_relationship.go
index b979ffdf8..90146b8a8 100644
--- a/pkg/topology/component_relationship.go
+++ b/pkg/topology/component_relationship.go
@@ -51,6 +51,15 @@ var ComponentRelationshipSync = &job.Job{
 			}
 			ctx.History.IncrSuccess()
 		}
+
+		// Cleanup dead relationships
+		componentIDsWithSelectors := lo.Map(components, func(c models.Component, _ int) string { return c.ID.String() })
+		if err := ctx.DB().Table("component_relationships").
+			Where("relationship_id NOT IN ?", componentIDsWithSelectors).
+			Update("deleted_at", duty.Now()).Error; err != nil {
+			return fmt.Errorf("error cleaning up dead component_relationships: %w", err)
+		}
+
 		return nil
 	},
 }