diff --git a/src/yuzu/configuration/configure_debug.cpp b/src/yuzu/configuration/configure_debug.cpp
index 5e66239ff..7fd07539a 100644
--- a/src/yuzu/configuration/configure_debug.cpp
+++ b/src/yuzu/configuration/configure_debug.cpp
@@ -44,5 +44,4 @@ void ConfigureDebug::applyConfiguration() {
     Log::Filter filter;
     filter.ParseFilterString(Settings::values.log_filter);
     Log::SetGlobalFilter(filter);
-    Settings::Apply();
 }
diff --git a/src/yuzu/configuration/configure_general.cpp b/src/yuzu/configuration/configure_general.cpp
index baa558667..cb7d3f8bf 100644
--- a/src/yuzu/configuration/configure_general.cpp
+++ b/src/yuzu/configuration/configure_general.cpp
@@ -44,5 +44,4 @@ void ConfigureGeneral::applyConfiguration() {
     Settings::values.use_cpu_jit = ui->use_cpu_jit->isChecked();
     Settings::values.use_multi_core = ui->use_multi_core->isChecked();
     Settings::values.use_docked_mode = ui->use_docked_mode->isChecked();
-    Settings::Apply();
 }
diff --git a/src/yuzu/configuration/configure_graphics.cpp b/src/yuzu/configuration/configure_graphics.cpp
index 7664880d5..3379b7963 100644
--- a/src/yuzu/configuration/configure_graphics.cpp
+++ b/src/yuzu/configuration/configure_graphics.cpp
@@ -67,5 +67,4 @@ void ConfigureGraphics::applyConfiguration() {
         ToResolutionFactor(static_cast<Resolution>(ui->resolution_factor_combobox->currentIndex()));
     Settings::values.toggle_framelimit = ui->toggle_framelimit->isChecked();
     Settings::values.use_accurate_framebuffers = ui->use_accurate_framebuffers->isChecked();
-    Settings::Apply();
 }
diff --git a/src/yuzu/configuration/configure_input.cpp b/src/yuzu/configuration/configure_input.cpp
index 78559e2bb..5e7badedf 100644
--- a/src/yuzu/configuration/configure_input.cpp
+++ b/src/yuzu/configuration/configure_input.cpp
@@ -191,8 +191,6 @@ void ConfigureInput::applyConfiguration() {
                    [](const Common::ParamPackage& param) { return param.Serialize(); });
     std::transform(analogs_param.begin(), analogs_param.end(), Settings::values.analogs.begin(),
                    [](const Common::ParamPackage& param) { return param.Serialize(); });
-
-    Settings::Apply();
 }
 
 void ConfigureInput::loadConfiguration() {
diff --git a/src/yuzu/main.cpp b/src/yuzu/main.cpp
index 75f8d1216..be38cfa9b 100644
--- a/src/yuzu/main.cpp
+++ b/src/yuzu/main.cpp
@@ -723,10 +723,12 @@ void GMainWindow::ToggleWindowMode() {
 
 void GMainWindow::OnConfigure() {
     ConfigureDialog configureDialog(this);
+    auto old_theme = UISettings::values.theme;
     auto result = configureDialog.exec();
     if (result == QDialog::Accepted) {
         configureDialog.applyConfiguration();
-        UpdateUITheme();
+        if (UISettings::values.theme != old_theme)
+            UpdateUITheme();
         config->Save();
     }
 }