diff --git a/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp b/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp
index a999a518af..909ce801a4 100644
--- a/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp
+++ b/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp
@@ -300,6 +300,26 @@ GraphicsSettingsWidget::GraphicsSettingsWidget(SettingsWindow* dialog, QWidget*
 	}
 #endif
 
+	// Get rid of widescreen/no-interlace checkboxes from per-game settings, unless the user previously had them set.
+	if (m_dialog->isPerGameSettings())
+	{
+		if ((m_dialog->containsSettingValue("EmuCore", "EnableWideScreenPatches") || m_dialog->containsSettingValue("EmuCore", "EnableNoInterlacingPatches")) &&
+			QMessageBox::question(QtUtils::GetRootWidget(this), tr("Remove Unsupported Settings"),
+				tr("You currently have the <strong>Enable Widescreen Patches</strong> or <strong>Enable No-Interlacing Patches</strong> options enabled for this game.<br><br>"
+				   "We no longer support these options, instead <strong>you should select the \"Patches\" section, and explicitly enable the patches you want.</strong><br><br>"
+				   "Do you want to remove these options from your game configuration now?"),
+				QMessageBox::Yes, QMessageBox::No) == QMessageBox::Yes)
+		{
+			m_dialog->removeSettingValue("EmuCore", "EnableWideScreenPatches");
+			m_dialog->removeSettingValue("EmuCore", "EnableNoInterlacingPatches");
+		}
+
+		m_ui.gridLayout->removeWidget(m_ui.widescreenPatches);
+		m_ui.gridLayout->removeWidget(m_ui.noInterlacingPatches);
+		safe_delete(m_ui.widescreenPatches);
+		safe_delete(m_ui.noInterlacingPatches);		
+	}
+
 	// Hide advanced options by default.
 	if (!QtHost::ShouldShowAdvancedSettings())
 	{
diff --git a/pcsx2-qt/Settings/GraphicsSettingsWidget.ui b/pcsx2-qt/Settings/GraphicsSettingsWidget.ui
index b96d21e460..923d07bb3a 100644
--- a/pcsx2-qt/Settings/GraphicsSettingsWidget.ui
+++ b/pcsx2-qt/Settings/GraphicsSettingsWidget.ui
@@ -324,7 +324,7 @@
         </layout>
        </item>
        <item row="8" column="0" colspan="2">
-        <layout class="QGridLayout" name="gridLayout_5">
+        <layout class="QGridLayout" name="displayGridLayout">
          <item row="3" column="0">
           <widget class="QCheckBox" name="PCRTCOffsets">
            <property name="text">
diff --git a/pcsx2/ImGui/FullscreenUI.cpp b/pcsx2/ImGui/FullscreenUI.cpp
index cbb20e10fb..95028ad424 100644
--- a/pcsx2/ImGui/FullscreenUI.cpp
+++ b/pcsx2/ImGui/FullscreenUI.cpp
@@ -3272,10 +3272,15 @@ void FullscreenUI::DrawGraphicsSettingsPage()
 		"EmuCore/GS", "StretchY", 100, 10, 300, FSUI_CSTR("%d%%"));
 	DrawIntRectSetting(bsi, FSUI_CSTR("Crop"), FSUI_CSTR("Crops the image, while respecting aspect ratio."), "EmuCore/GS", "CropLeft", 0,
 		"CropTop", 0, "CropRight", 0, "CropBottom", 0, 0, 720, 1, FSUI_CSTR("%dpx"));
-	DrawToggleSetting(bsi, FSUI_CSTR("Enable Widescreen Patches"), FSUI_CSTR("Enables loading widescreen patches from pnach files."),
-		"EmuCore", "EnableWideScreenPatches", false);
-	DrawToggleSetting(bsi, FSUI_CSTR("Enable No-Interlacing Patches"),
-		FSUI_CSTR("Enables loading no-interlacing patches from pnach files."), "EmuCore", "EnableNoInterlacingPatches", false);
+
+	if (!IsEditingGameSettings(bsi))
+	{
+		DrawToggleSetting(bsi, FSUI_CSTR("Enable Widescreen Patches"), FSUI_CSTR("Enables loading widescreen patches from pnach files."),
+			"EmuCore", "EnableWideScreenPatches", false);
+		DrawToggleSetting(bsi, FSUI_CSTR("Enable No-Interlacing Patches"),
+			FSUI_CSTR("Enables loading no-interlacing patches from pnach files."), "EmuCore", "EnableNoInterlacingPatches", false);
+	}
+
 	DrawIntListSetting(bsi, FSUI_CSTR("Bilinear Upscaling"), FSUI_CSTR("Smooths out the image when upscaling the console to the screen."),
 		"EmuCore/GS", "linear_present_mode", static_cast<int>(GSPostBilinearMode::BilinearSharp), s_bilinear_present_options,
 		std::size(s_bilinear_present_options), true);