diff --git a/Flatpak/org.DolphinEmu.dolphin-emu.yml b/Flatpak/org.DolphinEmu.dolphin-emu.yml
index 3ef6e940b1..4e2cbbe81d 100644
--- a/Flatpak/org.DolphinEmu.dolphin-emu.yml
+++ b/Flatpak/org.DolphinEmu.dolphin-emu.yml
@@ -44,6 +44,12 @@ modules:
   - name: dolphin-emu
     buildsystem: cmake-ninja
     builddir: true
+    build-options:
+      # don't use any default flags provided by the SDK
+      cflags: ""
+      cflags-override: true
+      cxxflags: ""
+      cxxflags-override: true
     config-opts:
       - -DCMAKE_BUILD_TYPE=Release
       - -DENABLE_ALSA=OFF