diff --git a/.changeset/late-insects-punch.md b/.changeset/late-insects-punch.md
new file mode 100644
index 0000000000..5ec64f7959
--- /dev/null
+++ b/.changeset/late-insects-punch.md
@@ -0,0 +1,5 @@
+---
+"@medusajs/medusa": patch
+---
+
+fix(medusa): model loader with customizations
diff --git a/packages/medusa/src/loaders/__tests__/models.spec.ts b/packages/medusa/src/loaders/__tests__/models.spec.ts
index 7d38ae836c..7ec8e5af54 100644
--- a/packages/medusa/src/loaders/__tests__/models.spec.ts
+++ b/packages/medusa/src/loaders/__tests__/models.spec.ts
@@ -12,7 +12,7 @@ describe("models loader", () => {
 
   beforeAll(async () => {
     try {
-      models = await modelsLoader({
+      models = modelsLoader({
         container,
         isTest: true,
         coreTestPathGlob: "../models/{product,product-variant}.ts",
@@ -30,9 +30,9 @@ describe("models loader", () => {
   })
 
   it("ensure that the product model is an extended model", () => {
-    const productModel = models.find((model) => model.name === "Product")
+    const productModel = container.resolve("productModel")
 
-    expect(new productModel().custom_attribute).toEqual("test")
+    expect(productModel.custom_attribute).toEqual("test")
   })
 
   it("ensure that the extended product model is registered in db_entities", () => {
diff --git a/packages/medusa/src/loaders/models.ts b/packages/medusa/src/loaders/models.ts
index 8d7ac29087..aba6c9d22a 100644
--- a/packages/medusa/src/loaders/models.ts
+++ b/packages/medusa/src/loaders/models.ts
@@ -8,6 +8,7 @@ import path from "path"
 import { ClassConstructor, MedusaContainer } from "../types/global"
 import { EntitySchema } from "typeorm"
 import { asClass, asValue } from "awilix"
+import { upperCaseFirst } from "@medusajs/utils"
 
 type ModelLoaderParams = {
   container: MedusaContainer
@@ -62,8 +63,9 @@ export default (
               // If an extension file is found, override it with that instead
               if (mappedExtensionModel) {
                 const coreModel = require(modelPath)
-                const modelName =
+                const modelName = upperCaseFirst(
                   formatRegistrationNameWithoutNamespace(modelPath)
+                )
 
                 coreModel[modelName] = mappedExtensionModel
                 val = mappedExtensionModel
diff --git a/packages/medusa/src/loaders/plugins.ts b/packages/medusa/src/loaders/plugins.ts
index 96301ad671..de6df5f2e3 100644
--- a/packages/medusa/src/loaders/plugins.ts
+++ b/packages/medusa/src/loaders/plugins.ts
@@ -1,4 +1,4 @@
-import { SearchUtils } from "@medusajs/utils"
+import { SearchUtils, upperCaseFirst } from "@medusajs/utils"
 import { aliasTo, asFunction, asValue, Lifetime } from "awilix"
 import { Express } from "express"
 import fs from "fs"
@@ -100,7 +100,7 @@ export default async ({
 function getResolvedPlugins(
   rootDirectory: string,
   configModule: ConfigModule,
-  extensionDirectoryPath: string = 'dist'
+  extensionDirectoryPath = "dist"
 ): undefined | PluginDetails[] {
   const { plugins } = configModule
 
@@ -132,8 +132,8 @@ export async function registerPluginModels({
   rootDirectory,
   container,
   configModule,
-  extensionDirectoryPath = 'dist',
-  pathGlob = "/models/*.js"
+  extensionDirectoryPath = "dist",
+  pathGlob = "/models/*.js",
 }: {
   rootDirectory: string
   container: MedusaContainer
@@ -141,20 +141,13 @@ export async function registerPluginModels({
   extensionDirectoryPath?: string
   pathGlob?: string
 }): Promise<void> {
-  const resolved = getResolvedPlugins(
-    rootDirectory,
-    configModule,
-    extensionDirectoryPath
-  ) || []
+  const resolved =
+    getResolvedPlugins(rootDirectory, configModule, extensionDirectoryPath) ||
+    []
 
   await Promise.all(
     resolved.map(async (pluginDetails) => {
-      registerModels(
-        pluginDetails,
-        container,
-        rootDirectory,
-        pathGlob,
-      )
+      registerModels(pluginDetails, container, rootDirectory, pathGlob)
     })
   )
 }
@@ -579,57 +572,74 @@ function registerRepositories(
  *    version, id, resolved path, etc. See resolvePlugin
  * @param {object} container - the container where the services will be
  *    registered
+ * @param rootDirectory
+ * @param pathGlob
  * @return {void}
  */
 function registerModels(
   pluginDetails: PluginDetails,
   container: MedusaContainer,
   rootDirectory: string,
-  pathGlob: string = "/models/*.js"
+  pathGlob = "/models/*.js"
 ): void {
-  const pluginFullPathGlob =  path.join(pluginDetails.resolve, pathGlob)
+  const pluginFullPathGlob = path.join(pluginDetails.resolve, pathGlob)
 
   const modelExtensionsMap = getModelExtensionsMap({
-    directory: rootDirectory,
+    directory: pluginDetails.resolve,
     pathGlob: pathGlob,
     config: { register: true },
   })
 
-  const coreOrPluginModelsPath = glob.sync(
-    pluginFullPathGlob,
-    { ignore: ["index.js", "index.js.map"] }
-  )
+  const pluginModels = glob.sync(pluginFullPathGlob, {
+    ignore: ["index.js", "index.js.map"],
+  })
 
-  coreOrPluginModelsPath.forEach((coreOrPluginModelPath) => {
+  const coreModelsFullGlob = path.join(__dirname, "../models/*.js")
+  const coreModels = glob.sync(coreModelsFullGlob, {
+    cwd: __dirname,
+    ignore: ["index.js", "index.ts", "index.js.map"],
+  })
+
+  // Apply the extended models to the core models first to ensure that
+  // when relationships are created, the extended models are used
+  coreModels.forEach((modelPath) => {
+    const loaded = require(modelPath) as
+      | ClassConstructor<unknown>
+      | EntitySchema
+
+    if (loaded) {
+      const name = formatRegistrationName(modelPath)
+      const mappedExtensionModel = modelExtensionsMap.get(name)
+      if (mappedExtensionModel) {
+        const modelName = upperCaseFirst(
+          formatRegistrationNameWithoutNamespace(modelPath)
+        )
+
+        loaded[modelName] = mappedExtensionModel
+      }
+    }
+  })
+
+  pluginModels.forEach((coreOrPluginModelPath) => {
     const loaded = require(coreOrPluginModelPath) as
       | ClassConstructor<unknown>
       | EntitySchema
 
-    Object.entries(loaded).map(
-      ([, val]: [string, ClassConstructor<unknown> | EntitySchema]) => {
-        if (typeof val === "function" || val instanceof EntitySchema) {
-          const name = formatRegistrationName(coreOrPluginModelPath)
-          const mappedExtensionModel = modelExtensionsMap.get(name)
+    if (loaded) {
+      Object.entries(loaded).map(
+        ([, val]: [string, ClassConstructor<unknown> | EntitySchema]) => {
+          if (typeof val === "function" || val instanceof EntitySchema) {
+            const name = formatRegistrationName(coreOrPluginModelPath)
 
-          // If an extension file is found, override it with that instead
-          if (mappedExtensionModel) {
-            const coreOrPluginModel = require(coreOrPluginModelPath)
-            const modelName = formatRegistrationNameWithoutNamespace(
-              coreOrPluginModelPath
-            )
+            container.register({
+              [name]: asValue(val),
+            })
 
-            coreOrPluginModel[modelName] = mappedExtensionModel
-            val = mappedExtensionModel
+            container.registerAdd("db_entities", asValue(val))
           }
-
-          container.register({
-            [name]: asValue(val),
-          })
-
-          container.registerAdd("db_entities", asValue(val))
         }
-      }
-    )
+      )
+    }
   })
 }