diff --git a/.github/workflows/flatpak.yml b/.github/workflows/flatpak.yml
index 93d3e58f..c829a862 100644
--- a/.github/workflows/flatpak.yml
+++ b/.github/workflows/flatpak.yml
@@ -14,6 +14,11 @@ jobs:
     - name: Configure flatpak
       run: flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
 
+    - name: Configure git
+      run: git config --global protocol.file.allow always
+      # Have to do this because for a while git's handling of submodules was broken
+      # See https://github.com/flatpak/flatpak-builder/issues/495
+
     - name: Checkout openchemistry
       uses: actions/checkout@v4
       with: