diff --git a/.changeset/honest-peaches-call.md b/.changeset/honest-peaches-call.md
new file mode 100644
index 0000000000..cc0e6c3652
--- /dev/null
+++ b/.changeset/honest-peaches-call.md
@@ -0,0 +1,7 @@
+---
+"@medusajs/modules-sdk": patch
+"@medusajs/medusa": patch
+"@medusajs/link-modules": patch
+---
+
+Fix custom modules loader
diff --git a/packages/link-modules/src/initialize/index.ts b/packages/link-modules/src/initialize/index.ts
index 8d6b6b56ee..d35dabc640 100644
--- a/packages/link-modules/src/initialize/index.ts
+++ b/packages/link-modules/src/initialize/index.ts
@@ -108,7 +108,7 @@ export const initialize = async (
     }
 
     const logger =
-      injectedDependencies?.[ContainerRegistrationKeys.LOGGER] ?? console.log
+      injectedDependencies?.[ContainerRegistrationKeys.LOGGER] ?? console
 
     definition.schema = generateGraphQLSchema(definition, primary, foreign, {
       logger,
diff --git a/packages/medusa/src/loaders/medusa-app.ts b/packages/medusa/src/loaders/medusa-app.ts
index af8cae1ccb..665bef8e67 100644
--- a/packages/medusa/src/loaders/medusa-app.ts
+++ b/packages/medusa/src/loaders/medusa-app.ts
@@ -10,6 +10,7 @@ import {
 import {
   CommonTypes,
   InternalModuleDeclaration,
+  LoadedModule,
   MedusaContainer,
   ModuleDefinition,
 } from "@medusajs/types"
@@ -54,12 +55,13 @@ export async function migrateMedusaApp(
   },
   config = { registerInContainer: true }
 ): Promise<void> {
-  const featureFlagRouter = container.resolve<FlagRouter>("featureFlagRouter")
-  const isMedusaV2Enabled = featureFlagRouter.isFeatureEnabled(MedusaV2Flag.key)
   const injectedDependencies = {
     [ContainerRegistrationKeys.PG_CONNECTION]: container.resolve(
       ContainerRegistrationKeys.PG_CONNECTION
     ),
+    [ContainerRegistrationKeys.LOGGER]: container.resolve(
+      ContainerRegistrationKeys.LOGGER
+    ),
   }
 
   const sharedResourcesConfig = {
@@ -73,7 +75,7 @@ export async function migrateMedusaApp(
 
   // Apply default options to legacy modules
   for (const moduleKey of Object.keys(configModules)) {
-    if (!ModulesDefinition[moduleKey].isLegacy) {
+    if (!ModulesDefinition[moduleKey]?.isLegacy) {
       continue
     }
 
@@ -121,6 +123,9 @@ export const loadMedusaApp = async (
     [ContainerRegistrationKeys.PG_CONNECTION]: container.resolve(
       ContainerRegistrationKeys.PG_CONNECTION
     ),
+    [ContainerRegistrationKeys.LOGGER]: container.resolve(
+      ContainerRegistrationKeys.LOGGER
+    ),
   }
 
   const sharedResourcesConfig = {
@@ -137,7 +142,7 @@ export const loadMedusaApp = async (
 
   // Apply default options to legacy modules
   for (const moduleKey of Object.keys(configModules)) {
-    if (!ModulesDefinition[moduleKey].isLegacy) {
+    if (!ModulesDefinition[moduleKey]?.isLegacy) {
       continue
     }
 
@@ -202,9 +207,10 @@ export const loadMedusaApp = async (
     asValue(medusaApp.query)
   )
 
-  for (const [serviceKey, moduleService] of Object.entries(medusaApp.modules)) {
+  for (const moduleService of Object.values(medusaApp.modules)) {
+    const loadedModule = moduleService as LoadedModule
     container.register(
-      ModulesDefinition[serviceKey].registrationName,
+      loadedModule.__definition.registrationName,
       asValue(moduleService)
     )
   }
diff --git a/packages/modules-sdk/src/medusa-module.ts b/packages/modules-sdk/src/medusa-module.ts
index 1d2cdd1e80..29cedd938a 100644
--- a/packages/modules-sdk/src/medusa-module.ts
+++ b/packages/modules-sdk/src/medusa-module.ts
@@ -18,6 +18,7 @@ import {
   simpleHash,
   stringifyCircular,
 } from "@medusajs/utils"
+import { EOL } from "os"
 import {
   moduleLoader,
   registerMedusaLinkModule,
@@ -312,6 +313,14 @@ export class MedusaModule {
           keyName
         ].__joinerConfig()
 
+        if (!joinerConfig.primaryKeys) {
+          logger.warn(
+            `Primary keys are not defined by the module ${keyName}. Setting default primary key to 'id'${EOL}`
+          )
+
+          joinerConfig.primaryKeys = ["id"]
+        }
+
         services[keyName].__joinerConfig = joinerConfig
         MedusaModule.setJoinerConfig(keyName, joinerConfig)
       }