diff --git a/.github/workflows/linux_build_flatpak.yml b/.github/workflows/linux_build_flatpak.yml
index 7f980ffe5dd666..77a2e29db3bdb0 100644
--- a/.github/workflows/linux_build_flatpak.yml
+++ b/.github/workflows/linux_build_flatpak.yml
@@ -58,6 +58,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
+          set-safe-directory: ${{ env.GITHUB_WORKSPACE }}
 
       # Hackity hack. When running the workflow on a schedule, we don't have the tag,
       # it doesn't fetch tags, therefore we don't get a version. So grab them manually.
@@ -91,6 +92,7 @@ jobs:
 
       - name: Generate AppStream XML
         run: |
+          git config --global --add safe.directory /__w/pcsx2/pcsx2
           ./.github/workflows/scripts/linux/generate-metainfo.sh .github/workflows/scripts/linux/flatpak/net.pcsx2.PCSX2.metainfo.xml
           cat .github/workflows/scripts/linux/flatpak/net.pcsx2.PCSX2.metainfo.xml
           flatpak-builder-lint appstream .github/workflows/scripts/linux/flatpak/net.pcsx2.PCSX2.metainfo.xml
diff --git a/.github/workflows/scripts/linux/generate-metainfo.sh b/.github/workflows/scripts/linux/generate-metainfo.sh
index ee263c05eb3a8c..33b8f42359e6f4 100755
--- a/.github/workflows/scripts/linux/generate-metainfo.sh
+++ b/.github/workflows/scripts/linux/generate-metainfo.sh
@@ -7,8 +7,6 @@ if [[ $# -lt 1 ]]; then
 	exit 1
 fi
 
-git config --global --add safe.directory /__w/pcsx2/pcsx2
-
 OUTFILE=$1
 GIT_DATE=$(git log -1 --pretty=%cd --date=iso8601)
 GIT_VERSION=$(git tag --points-at HEAD)