diff --git a/.github/workflows/flatpak.yml b/.github/workflows/flatpak.yml
index cc8d7ba9..25d27411 100644
--- a/.github/workflows/flatpak.yml
+++ b/.github/workflows/flatpak.yml
@@ -11,53 +11,10 @@ jobs:
       options: --privileged
 
     steps:
-    - name: Checkout openchemistry
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/openchemistry
-        submodules: false
-        path: src
-        
     - name: Checkout avogadroapp
       uses: actions/checkout@v4
       with:
-        path: src/avogadroapp
-        
-    - name: Checkout avogadrolibs
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/avogadrolibs
-        path: src/avogadrolibs
-
-    - name: Checkout i18n
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/avogadro-i18n
-        path: src/avogadro-i18n
-    
-    - name: Checkout avogadrogenerators
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/avogenerators
-        path: src/avogadrogenerators
-
-    - name: Checkout crystals
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/crystals
-        path: src/crystals
-
-    - name: Checkout fragments
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/fragments
-        path: src/fragments
-
-    - name: Checkout molecules
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/molecules
-        path: src/molecules
+        path: avogadroapp
 
     - name: Checkout Flathub shared-modules
       uses: actions/checkout@v4
diff --git a/flatpak/org.openchemistry.Avogadro2.yaml b/flatpak/org.openchemistry.Avogadro2.yaml
index 30305451..413efd1f 100644
--- a/flatpak/org.openchemistry.Avogadro2.yaml
+++ b/flatpak/org.openchemistry.Avogadro2.yaml
@@ -46,11 +46,49 @@ modules:
       - -DQT_VERSION=6
       - -DDOWNLOAD_TO_SOURCE_DIR=ON
     sources:
-      # Avogadro stuff all already collected together as part of GitHub Actions
-      # This means that if using this to build the Flatpak locally, the openchemistry repo and
-      # its submodules must be cloned into ./src in advance of running flatpak-builder with this manifest
-      - type: dir
-        path: src
+      # First get the umbrella repo so we can use superbuild strategy
+      # Clone but not recursively, only want CMake files and dir structure
+      - type: git
+        url: https://github.com/OpenChemistry/openchemistry.git
+        commit: 0bd11984cdb6d8ecb13c255b7557dd8b3f0ef20d
+        disable-shallow-clone: true
+        disable-submodules: true
+
+      # Do the equivalent of checking out each in-house module
+      # avogadro-i18n
+      - type: git
+        url: https://github.com/OpenChemistry/avogadro-i18n.git
+        branch: master
+        dest: avogadro-i18n
+      # avogadroapp
+      - type: dir  # Use local folder checked out by GHA
+        path: avogadroapp
+        dest: avogadroapp
+      # avogadrogenerators
+      - type: git
+        url: https://github.com/OpenChemistry/avogenerators.git
+        branch: master
+        dest: avogadrogenerators
+      # avogadrolibs
+      - type: git
+        url: https://github.com/OpenChemistry/avogadrolibs.git
+        branch: master
+        dest: avogadrolibs
+      # crystals
+      - type: git
+        url: https://github.com/OpenChemistry/crystals.git
+        branch: master
+        dest: crystals
+      # fragments
+      - type: git
+        url: https://github.com/OpenChemistry/fragments.git
+        branch: main
+        dest: fragments
+      # molecules
+      - type: git
+        url: https://github.com/OpenChemistry/molecules.git
+        branch: master
+        dest: molecules
 
       # Now fetch third-party stuff where the source is expected in `openchemistry/thirdparty`
       # VTK