diff --git a/.changeset/cyan-taxis-behave.md b/.changeset/cyan-taxis-behave.md
new file mode 100644
index 0000000000..860f461484
--- /dev/null
+++ b/.changeset/cyan-taxis-behave.md
@@ -0,0 +1,6 @@
+---
+"@medusajs/link-modules": patch
+"@medusajs/modules-sdk": patch
+---
+
+feat(medusa-app): Link initialization should respect migrationOnly flag
diff --git a/packages/core/modules-sdk/src/medusa-app.ts b/packages/core/modules-sdk/src/medusa-app.ts
index 5dc5a08199..1123aefb8e 100644
--- a/packages/core/modules-sdk/src/medusa-app.ts
+++ b/packages/core/modules-sdk/src/medusa-app.ts
@@ -204,6 +204,7 @@ async function initializeLinks({
   linkModules,
   injectedDependencies,
   moduleExports,
+  migrationOnly = false,
 }) {
   try {
     let resources = moduleExports
@@ -220,7 +221,9 @@ async function initializeLinks({
     const linkResolution = await initialize(
       config,
       linkModules,
-      injectedDependencies
+      injectedDependencies,
+      undefined,
+      migrationOnly
     )
 
     return {
@@ -488,6 +491,7 @@ async function MedusaApp_({
     linkModules,
     injectedDependencies,
     moduleExports: isMedusaModule(linkModule) ? linkModule : undefined,
+    migrationOnly,
   })
 
   const loadedSchema = getLoadedSchema()
diff --git a/packages/core/modules-sdk/src/medusa-module.ts b/packages/core/modules-sdk/src/medusa-module.ts
index cc8c2c68f9..d24317bd10 100644
--- a/packages/core/modules-sdk/src/medusa-module.ts
+++ b/packages/core/modules-sdk/src/medusa-module.ts
@@ -90,6 +90,7 @@ export type LinkModuleBootstrapOptions = {
   moduleExports?: ModuleExports
   injectedDependencies?: Record<string, any>
   cwd?: string
+  migrationOnly?: boolean
 }
 
 export type RegisterModuleJoinerConfig =
@@ -652,6 +653,7 @@ class MedusaModule {
     moduleExports,
     injectedDependencies,
     cwd,
+    migrationOnly,
   }: LinkModuleBootstrapOptions): Promise<{
     [key: string]: unknown
   }> {
@@ -720,6 +722,7 @@ class MedusaModule {
       await moduleLoader({
         container,
         moduleResolutions,
+        migrationOnly,
         logger: logger_,
       })
     } catch (err) {
diff --git a/packages/modules/link-modules/src/initialize/index.ts b/packages/modules/link-modules/src/initialize/index.ts
index a74adb5209..6990bcd453 100644
--- a/packages/modules/link-modules/src/initialize/index.ts
+++ b/packages/modules/link-modules/src/initialize/index.ts
@@ -34,7 +34,8 @@ export const initialize = async (
     | InternalModuleDeclaration,
   pluginLinksDefinitions?: ModuleJoinerConfig[],
   injectedDependencies?: InitializeModuleInjectableDependencies,
-  cwd?: string
+  cwd?: string,
+  migrationOnly?: boolean
 ): Promise<{ [link: string]: ILinkModule }> => {
   const allLinks = {}
   const modulesLoadedKeys = MedusaModule.getLoadedModules().map(
@@ -170,6 +171,7 @@ export const initialize = async (
         moduleExports: moduleDefinition,
         injectedDependencies,
         cwd,
+        migrationOnly,
       })
 
       allLinks[serviceKey as string] = Object.values(loaded)[0]