diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3c1b732f9d..d782a296e9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -108,6 +108,7 @@ build-retroarch-linux-x64:
     - "./configure --prefix=/usr"
     - "make -j$NUMPROC"
     - "make install DESTDIR=${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDirQt prefix=/usr"
+    - "rm -rf ${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDirQt/etc"
     - "cd ${MEDIA_PATH}/${CI_PROJECT_NAME}/ && tar -czf AppDirQt.tar.gz AppDirQt && rm -rf AppDirQt && cd -"
     - "mv -f retroarch retroarch_qt"
     # Non-Qt build
@@ -116,6 +117,7 @@ build-retroarch-linux-x64:
     - "./configure --disable-qt --prefix=/usr"
     - "make -j$NUMPROC"
     - "make install DESTDIR=${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDir prefix=/usr"
+    - "rm -rf ${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDir/etc"
     - "cd ${MEDIA_PATH}/${CI_PROJECT_NAME}/ && tar -czf AppDir.tar.gz AppDir && rm -rf AppDir && cd -"
     # Filters
     - "mkdir -p ${MEDIA_PATH}/${CI_PROJECT_NAME}/filters/audio"
@@ -146,6 +148,7 @@ build-retroarch-linux-i686:
     - "./configure --prefix=/usr"
     - "make -j$NUMPROC"
     - "make install DESTDIR=${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDirQt prefix=/usr"
+    - "rm -rf ${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDirQt/etc"
     - "cd ${MEDIA_PATH}/${CI_PROJECT_NAME}/ && tar -czf AppDirQt.tar.gz AppDirQt && rm -rf AppDirQt && cd -"
     - "mv -f retroarch retroarch_qt"
     # Non-Qt build
@@ -154,6 +157,7 @@ build-retroarch-linux-i686:
     - "./configure --disable-qt --prefix=/usr"
     - "make -j$NUMPROC"
     - "make install DESTDIR=${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDir prefix=/usr"
+    - "rm -rf ${MEDIA_PATH}/${CI_PROJECT_NAME}/AppDir/etc"
     - "cd ${MEDIA_PATH}/${CI_PROJECT_NAME}/ && tar -czf AppDir.tar.gz AppDir && rm -rf AppDir && cd -"
     # Filters
     - "mkdir -p ${MEDIA_PATH}/${CI_PROJECT_NAME}/filters/audio"