diff --git a/src/yuzu/configuration/configure_system.cpp b/src/yuzu/configuration/configure_system.cpp
index 36920b1ff9..568f29518b 100644
--- a/src/yuzu/configuration/configure_system.cpp
+++ b/src/yuzu/configuration/configure_system.cpp
@@ -131,6 +131,11 @@ void ConfigureSystem::Setup(const ConfigurationShared::Builder& builder) {
     push(Settings::values.linkage.by_category[Settings::Category::System]);
 
     for (auto setting : settings) {
+        if (setting->Id() == Settings::values.program_args.Id()
+            || setting->Id() == Settings::values.debug_knobs.Id()) {
+            continue;
+        }
+
         if (setting->Id() == Settings::values.use_docked_mode.Id() &&
             Settings::IsConfiguringGlobal()) {
             continue;