diff --git a/.github/workflows/linux_build_flatpak.yml b/.github/workflows/linux_build_flatpak.yml
index 99b61597f8188d..7f980ffe5dd666 100644
--- a/.github/workflows/linux_build_flatpak.yml
+++ b/.github/workflows/linux_build_flatpak.yml
@@ -97,7 +97,7 @@ jobs:
 
       - name: Validate manifest
         run: |
-          flatpak-builder-lint org.flatpak.Builder manifest .github/workflows/scripts/linux/flatpak/net.pcsx2.PCSX2.json
+          flatpak-builder-lint manifest .github/workflows/scripts/linux/flatpak/net.pcsx2.PCSX2.json
 
       - name: Build Flatpak
         uses: flathub-infra/flatpak-github-actions/flatpak-builder@23796715b3dfa4c86ddf50cf29c3cc8b3c82dca8
@@ -116,7 +116,7 @@ jobs:
 
       - name: Validate build
         run: |
-          flatpak-builder-lint org.flatpak.Builder --exceptions repo flatpak_app
+          flatpak-builder-lint repo flatpak_app
 
       - name: Push to Flathub beta
         if: inputs.publish == true && inputs.branch == 'beta'