diff --git a/.github/workflows/setup_environment.yml b/.github/workflows/setup_environment.yml
index 067f9c8415..985d7d48bb 100644
--- a/.github/workflows/setup_environment.yml
+++ b/.github/workflows/setup_environment.yml
@@ -97,6 +97,15 @@ jobs:
         submodules: recursive
         fetch-depth: 0
 
+    - name: Remove thirparty submodules
+      run: |
+        if [[ "${{ inputs.qmake_extra }}" =~ "use_system_quazip" ]]; then
+          rm -rf thirdparty/quazip/quazip
+        fi
+        if [[ "${{ inputs.qmake_extra }}" =~ "use_system_qscintilla2" ]]; then
+          rm -rf thirdparty/qscintilla
+        fi
+
     - name: Set up environment
       run: buildScripts/github/install.sh
       env: