--- a/toolkit/components/extensions/Extension.jsm
+++ b/toolkit/components/extensions/Extension.jsm
@@ -886,17 +886,20 @@ ExtensionData.prototype = {
       let normalized = Schemas.normalize(this.manifest, "manifest.WebExtensionManifest", context);
       if (normalized.error) {
         this.manifestError(normalized.error);
       } else {
         this.manifest = normalized.value;
       }
 
       try {
-        this.id = this.manifest.applications.gecko.id;
+        // Do not override the add-on id that has been already assigned.
+        if (!this.id && this.manifest.applications.gecko.id) {
+          this.id = this.manifest.applications.gecko.id;
+        }
       } catch (e) {
         // Errors are handled by the type checks above.
       }
 
       return this.manifest;
     });
   },