diff --git a/generators/jdl/__snapshots__/generator.spec.ts.snap b/generators/jdl/__snapshots__/generator.spec.ts.snap
index 444c8d820ce7..491f271792a8 100644
--- a/generators/jdl/__snapshots__/generator.spec.ts.snap
+++ b/generators/jdl/__snapshots__/generator.spec.ts.snap
@@ -62,7 +62,6 @@ exports[`generator - jdl for application jdl with valid jdl should write expecte
   ".yo-rc.json": {
     "contents": "{
   "generator-jhipster": {
-    "applicationIndex": 0,
     "baseName": "jhipster",
     "entities": []
   }
@@ -109,7 +108,6 @@ exports[`generator - jdl for one application and entity jdl with valid jdl shoul
   ".yo-rc.json": {
     "contents": "{
   "generator-jhipster": {
-    "applicationIndex": 0,
     "baseName": "jhipster",
     "entities": [
       "Foo"
@@ -254,7 +252,6 @@ exports[`generator - jdl with a gateway generating json should generate expected
   ".yo-rc.json": {
     "contents": "{
   "generator-jhipster": {
-    "applicationIndex": 0,
     "applicationType": "gateway",
     "applications": {
       "ms": {}
diff --git a/generators/jdl/generator.spec.ts b/generators/jdl/generator.spec.ts
index 5e54684e1f6f..7a74f7f1ff30 100644
--- a/generators/jdl/generator.spec.ts
+++ b/generators/jdl/generator.spec.ts
@@ -174,7 +174,6 @@ describe(`generator - ${generator}`, () => {
   ".yo-rc.json": {
     "contents": "{
   "generator-jhipster": {
-    "applicationIndex": 0,
     "baseName": "jhipster",
     "blueprints": [
       {
diff --git a/generators/jdl/generator.ts b/generators/jdl/generator.ts
index 5b3634a7a204..0329855f21ca 100644
--- a/generators/jdl/generator.ts
+++ b/generators/jdl/generator.ts
@@ -174,8 +174,8 @@ export default class JdlGenerator extends BaseGenerator {
               app.sharedFs = createMemFs();
             }
           }
+          addApplicationIndex(this.applications);
         }
-        addApplicationIndex(this.applications);
         customizeForMicroservices(this.exportedApplicationsWithEntities);
       },
       async generateJson() {