diff --git a/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/impl/registry/sync/DynamicRegistriesImpl.java b/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/impl/registry/sync/DynamicRegistriesImpl.java
index dacbb565d6..83c5f41206 100644
--- a/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/impl/registry/sync/DynamicRegistriesImpl.java
+++ b/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/impl/registry/sync/DynamicRegistriesImpl.java
@@ -35,6 +35,7 @@
 
 public final class DynamicRegistriesImpl {
 	private static final List<RegistryLoader.Entry<?>> DYNAMIC_REGISTRIES = new ArrayList<>(RegistryLoader.DYNAMIC_REGISTRIES);
+	public static final Set<RegistryKey<?>> FABRIC_DYNAMIC_REGISTRY_KEYS = new HashSet<>();
 	public static final Set<RegistryKey<? extends Registry<?>>> DYNAMIC_REGISTRY_KEYS = new HashSet<>();
 	public static final Set<RegistryKey<? extends Registry<?>>> SKIP_EMPTY_SYNC_REGISTRIES = new HashSet<>();
 
@@ -61,6 +62,7 @@ public static <T> void register(RegistryKey<? extends Registry<T>> key, Codec<T>
 
 		var entry = new RegistryLoader.Entry<>(key, codec);
 		DYNAMIC_REGISTRIES.add(entry);
+		FABRIC_DYNAMIC_REGISTRY_KEYS.add(key);
 	}
 
 	public static <T> void addSyncedRegistry(RegistryKey<? extends Registry<T>> registryKey, Codec<T> networkCodec, DynamicRegistries.SyncOption... options) {
diff --git a/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/mixin/registry/sync/RegistryLoaderMixin.java b/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/mixin/registry/sync/RegistryLoaderMixin.java
index 33f93359e3..550b923ade 100644
--- a/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/mixin/registry/sync/RegistryLoaderMixin.java
+++ b/fabric-registry-sync-v0/src/main/java/net/fabricmc/fabric/mixin/registry/sync/RegistryLoaderMixin.java
@@ -37,6 +37,7 @@
 import net.minecraft.util.Identifier;
 
 import net.fabricmc.fabric.api.event.registry.DynamicRegistrySetupCallback;
+import net.fabricmc.fabric.impl.registry.sync.DynamicRegistriesImpl;
 import net.fabricmc.fabric.impl.registry.sync.DynamicRegistryViewImpl;
 
 @Mixin(RegistryLoader.class)
@@ -61,11 +62,12 @@ private static void beforeLoad(ResourceManager resourceManager, DynamicRegistryM
 	}
 
 	// Vanilla doesn't mark namespaces in the directories of dynamic registries at all,
-	// so we prepend the directories with the namespace if it's a modded registry id.
+	// so we prepend the directories with the namespace if it's a modded registry registered using the Fabric API.
 	@Inject(method = "getPath", at = @At("RETURN"), cancellable = true)
 	private static void prependDirectoryWithNamespace(Identifier id, CallbackInfoReturnable<String> info) {
-		if (!id.getNamespace().equals(Identifier.DEFAULT_NAMESPACE)) {
-			String newPath = id.getNamespace() + "/" + info.getReturnValue();
+		if (!id.getNamespace().equals(Identifier.DEFAULT_NAMESPACE)
+				&& DynamicRegistriesImpl.FABRIC_DYNAMIC_REGISTRY_KEYS.contains(RegistryKey.ofRegistry(id))) {
+			final String newPath = id.getNamespace() + "/" + info.getReturnValue();
 			info.setReturnValue(newPath);
 		}
 	}