diff --git a/.changeset/mean-rockets-worry.md b/.changeset/mean-rockets-worry.md
new file mode 100644
index 0000000000..0cc715faa6
--- /dev/null
+++ b/.changeset/mean-rockets-worry.md
@@ -0,0 +1,5 @@
+---
+"@medusajs/index": patch
+---
+
+fix(index): preserve existing fields configuration (#13639)
diff --git a/packages/modules/index/src/utils/build-config.ts b/packages/modules/index/src/utils/build-config.ts
index 515bc155cc..c7e1b599e1 100644
--- a/packages/modules/index/src/utils/build-config.ts
+++ b/packages/modules/index/src/utils/build-config.ts
@@ -845,7 +845,9 @@ function processEntity(
           ]
           intermediateEntityObjectRepresentationRef.moduleConfig =
             intermediateEntityModule
-          intermediateEntityObjectRepresentationRef.fields = ["id"]
+          if (!intermediateEntityObjectRepresentationRef.fields.includes("id")) {
+            intermediateEntityObjectRepresentationRef.fields.push("id")
+          }
 
           /**
            * We push the parent id only between intermediate entities but not between intermediate and link