diff --git a/.github/workflows/flatpak.yml b/.github/workflows/flatpak.yml
new file mode 100644
index 0000000000..a47d264fa8
--- /dev/null
+++ b/.github/workflows/flatpak.yml
@@ -0,0 +1,101 @@
+name: Build Flatpak
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  flatpak:
+    name: "Flatpak"
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Install dependencies
+      run: sudo apt update -qq && sudo apt install -y -qq flatpak flatpak-builder
+    
+    - 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:
+        repository: openchemistry/openchemistry
+        submodules: false
+        path: openchemistry
+        
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadroapp
+        
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v4
+      with:
+        path: openchemistry/avogadrolibs
+
+    - name: Checkout i18n
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: openchemistry/avogadro-i18n
+    
+    - name: Checkout avogadrogenerators
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogenerators
+        path: openchemistry/avogadrogenerators
+
+    - name: Checkout crystals
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/crystals
+        path: openchemistry/crystals
+
+    - name: Checkout fragments
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/fragments
+        path: openchemistry/fragments
+
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: openchemistry/molecules
+
+    - name: Checkout Flathub shared-modules
+      uses: actions/checkout@v4
+      with:
+        repository: flathub/shared-modules
+        path: shared-modules
+
+    - name: Set up tmate session
+      if: failure()
+      uses: mxschmitt/action-tmate@v3
+
+    - name: Move manifest
+      run: mv openchemistry/avogadroapp/flatpak/org.openchemistry.Avogadro2.yaml ./
+
+    - name: Build with flatpak-builder
+      run: flatpak-builder --force-clean --user --install-deps-from=flathub --arch=x86_64 --default-branch=test --repo=repo builddir org.openchemistry.Avogadro2.yaml
+
+    - name: Create bundle
+      run: flatpak build-bundle repo Avogadro2.flatpak org.openchemistry.Avogadro2 test
+
+    - name: Upload bundle
+      uses: actions/upload-artifact@v4
+      with:
+        path: Avogadro2.flatpak
+    
+    - name: Cleanup
+      if: ${{ always() }} # To ensure this step runs even when earlier steps fail
+      shell: bash
+      run: |
+        ls -la ./
+        rm -rf ./* || true
+        rm -rf ./.??* || true
+        ls -la ./