diff --git a/com.xargon.retrodeck.yml b/com.xargon.retrodeck.yml
index 09241e47..332505a9 100644
--- a/com.xargon.retrodeck.yml
+++ b/com.xargon.retrodeck.yml
@@ -985,9 +985,9 @@ modules:
         - cp retrodeck.sh /app/bin/retrodeck.sh
         - chmod +x /app/bin/retrodeck.sh
 
-        # Configuring Yuzu
-        - mkdir -p /var/config/yuzu/
-        - cp qt-config.ini /var/config/yuzu/qt-config.ini
+	      # Yuzu
+        - mkdir -p ${FLATPAK_DEST}/retrodeck/emu-configs
+        - cp qt-config.ini ${FLATPAK_DEST}/retrodeck/emu-configs
 
         # Desktop entry
         - cp com.xargon.retrodeck.desktop /app/share/applications/com.xargon.retrodeck.desktop
diff --git a/retrodeck.sh b/retrodeck.sh
index 26feea8c..3a603d87 100755
--- a/retrodeck.sh
+++ b/retrodeck.sh
@@ -74,10 +74,13 @@ then
     mkdir -p /var/config/retroarch/cores/
     cp /app/share/libretro/cores/* /var/config/retroarch/cores/
 
-    # Initializing Yuzu
-    mkdir -p ~/retrodeck/bios/switch/keys
+    # Yuzu
+    mkdir -p ~/retrodeck/bios/switch/
+    mkdir -p /var/config/yuzu/keys
+    mkdir -p /var/data/yuzu/registered
     ln -s ~/retrodeck/bios/switch/keys /var/data/yuzu/keys
     ln -s /var/data/yuzu/registered ~/retrodeck/bios/switch/registered
+    cp /var/config/retroarch/emu-configs/qt-config.ini /var/config/yuzu/qt-config.ini
 
     touch ~/retrodeck/.lock