diff --git a/internal/store/builder.go b/internal/store/builder.go
index 5c38857d7b..b538305eaf 100644
--- a/internal/store/builder.go
+++ b/internal/store/builder.go
@@ -195,6 +195,14 @@ func (b *Builder) DefaultGenerateCustomResourceStoresFunc() ksmtypes.BuildCustom
 
 // WithCustomResourceStoreFactories returns configures a custom resource stores factory
 func (b *Builder) WithCustomResourceStoreFactories(fs ...customresource.RegistryFactory) {
+	obsoleteCustomResource := map[string]bool{}
+	for k := range availableStores {
+		if notCustomResource(k) {
+			continue
+		}
+		obsoleteCustomResource[k] = true
+	}
+
 	for i := range fs {
 		f := fs[i]
 		gvr := util.GVRFromType(f.Name(), f.ExpectedType())
@@ -207,6 +215,7 @@ func (b *Builder) WithCustomResourceStoreFactories(fs ...customresource.Registry
 		if _, ok := availableStores[gvrString]; ok {
 			klog.InfoS("Updating store", "GVR", gvrString)
 		}
+		obsoleteCustomResource[f.Name()] = false
 		availableStores[gvrString] = func(b *Builder) []cache.Store {
 			return b.buildCustomResourceStoresFunc(
 				f.Name(),
@@ -217,6 +226,11 @@ func (b *Builder) WithCustomResourceStoreFactories(fs ...customresource.Registry
 			)
 		}
 	}
+	for k, v := range obsoleteCustomResource {
+		if v {
+			delete(availableStores, k)
+		}
+	}
 }
 
 // allowList validates the given map and checks if the resources exists.
@@ -616,3 +630,7 @@ func cacheStoresToMetricStores(cStores []cache.Store) []*metricsstore.MetricsSto
 
 	return mStores
 }
+
+func notCustomResource(name string) bool {
+	return resourceExists(name)
+}