diff --git a/.github/workflows/cron_publish_flatpak.yml b/.github/workflows/cron_publish_flatpak.yml
index 59a3dcd908..505adf2611 100644
--- a/.github/workflows/cron_publish_flatpak.yml
+++ b/.github/workflows/cron_publish_flatpak.yml
@@ -4,6 +4,17 @@ on:
   schedule:
     - cron: "0 0 * * *" # Every day at 12am UTC.
   workflow_dispatch: # As well as manually.
+    inputs:
+      stableBuild:
+        description: Build and or publish to flathub stable or beta?
+        required: true
+        type: boolean
+        default: false
+      ref:
+        description: The git ref to build and or publish.
+        required: true
+        type: string 
+        default: master
 
 jobs:
 
@@ -54,6 +65,7 @@ jobs:
       cmakeflags: ""
       publish: true
       fetchTags: true
-      stableBuild: false
+      stableBuild: ${{ inputs.stableBuild || 'false' }}
+      ref: ${{ inputs.ref|| 'master' }}
     secrets: inherit
 
diff --git a/.github/workflows/linux_build_flatpak.yml b/.github/workflows/linux_build_flatpak.yml
index bf02d89c88..6ba9885515 100644
--- a/.github/workflows/linux_build_flatpak.yml
+++ b/.github/workflows/linux_build_flatpak.yml
@@ -39,6 +39,10 @@ on:
         required: false
         type: boolean
         default: false
+      ref:
+        required: false
+        type: string
+        default: master
 
 jobs:
   build_linux:
@@ -58,6 +62,7 @@ jobs:
           # This is required for the tagging logic in generate-metainfo.sh
           fetch-depth: 10
           fetch-tags: true
+          ref: ${{ inputs.ref }}
 
       # Work around container ownership issue
       - name: Set Safe Directory
diff --git a/.github/workflows/release_cut_new.yml b/.github/workflows/release_cut_new.yml
index 618f89fa5e..06ba5031d5 100644
--- a/.github/workflows/release_cut_new.yml
+++ b/.github/workflows/release_cut_new.yml
@@ -114,7 +114,9 @@ jobs:
       artifactPrefixName: "PCSX2-linux-Qt-x64-flatpak"
       compiler: clang
       cmakeflags: ""
-      publish: false
+      # Publish if we are creating a stable release
+      # The flathub cron job only picks up dev builds
+      publish: ${{ github.event_name == 'workflow_dispatch' && inputs.is_prelease == 'false' }}
       fetchTags: true
       stableBuild: ${{ github.event_name == 'workflow_dispatch' && inputs.is_prelease == 'false' }}
     secrets: inherit