diff --git a/.ci_scripts/install_dependencies.sh b/.ci_scripts/install_dependencies.sh
index 3b106617bb..0f3979e897 100755
--- a/.ci_scripts/install_dependencies.sh
+++ b/.ci_scripts/install_dependencies.sh
@@ -90,7 +90,7 @@ elif [ "$BUILD_TARGET" == "flatpak" ]
 then
   sudo apt-get update && sudo apt-get -y install flatpak-builder
   sudo flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
-  sudo flatpak-builder repo com.github.keriew.augustus.json --install-deps-from=flathub --install-deps-only --delete-build-dirs
+  sudo flatpak-builder repo res/com.github.keriew.augustus.json --install-deps-from=flathub --install-deps-only --delete-build-dirs
   sudo rm -R .flatpak-builder
 elif [ ! -z "$SDL_VERSION" ] && [ ! -z "$SDL_MIXER_VERSION" ]
 then
diff --git a/.ci_scripts/run_build.sh b/.ci_scripts/run_build.sh
index bde1e3148b..abbd76e61f 100755
--- a/.ci_scripts/run_build.sh
+++ b/.ci_scripts/run_build.sh
@@ -25,7 +25,7 @@ case "$BUILD_TARGET" in
 	fi
 	;;
 "flatpak")
-	flatpak-builder repo com.github.keriew.augustus.json --install-deps-from=flathub --keep-build-dirs
+	flatpak-builder repo res/com.github.keriew.augustus.json --install-deps-from=flathub --keep-build-dirs
 	cp .flatpak-builder/build/augustus/res/version.txt res/version.txt
 	;;
 "appimage")
diff --git a/com.github.keriew.augustus.json b/res/com.github.keriew.augustus.json
similarity index 100%
rename from com.github.keriew.augustus.json
rename to res/com.github.keriew.augustus.json