diff --git a/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp b/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp
index f8da272708..c8fc947064 100644
--- a/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp
+++ b/pcsx2-qt/Settings/GraphicsSettingsWidget.cpp
@@ -141,8 +141,8 @@ GraphicsSettingsWidget::GraphicsSettingsWidget(SettingsDialog* dialog, QWidget*
 	// HW Renderer Fixes
 	//////////////////////////////////////////////////////////////////////////
 	SettingWidgetBinder::BindWidgetToIntSetting(sif, m_ui.halfScreenFix, "EmuCore/GS", "UserHacks_Half_Bottom_Override", -1, -1);
-	SettingWidgetBinder::BindWidgetToIntSetting(sif, m_ui.skipDrawRangeStart, "EmuCore/GS", "UserHacks_SkipDraw", 0);
-	SettingWidgetBinder::BindWidgetToIntSetting(sif, m_ui.skipDrawRangeCount, "EmuCore/GS", "UserHacks_SkipDraw_Offset", 0);
+	SettingWidgetBinder::BindWidgetToIntSetting(sif, m_ui.skipDrawStart, "EmuCore/GS", "UserHacks_SkipDraw_Offset", 0);
+	SettingWidgetBinder::BindWidgetToIntSetting(sif, m_ui.skipDrawEnd, "EmuCore/GS", "UserHacks_SkipDraw", 0);
 	SettingWidgetBinder::BindWidgetToBoolSetting(sif, m_ui.hwAutoFlush, "EmuCore/GS", "UserHacks_AutoFlush", false);
 	SettingWidgetBinder::BindWidgetToBoolSetting(sif, m_ui.frameBufferConversion, "EmuCore/GS", "UserHacks_CPU_FB_Conversion", false);
 	SettingWidgetBinder::BindWidgetToBoolSetting(sif, m_ui.disableDepthEmulation, "EmuCore/GS", "UserHacks_DisableDepthSupport", false);
diff --git a/pcsx2-qt/Settings/GraphicsSettingsWidget.ui b/pcsx2-qt/Settings/GraphicsSettingsWidget.ui
index 784119deb8..7bc6122a15 100644
--- a/pcsx2-qt/Settings/GraphicsSettingsWidget.ui
+++ b/pcsx2-qt/Settings/GraphicsSettingsWidget.ui
@@ -586,7 +586,7 @@
          <item row="1" column="1">
           <widget class="QCheckBox" name="enableHWFixes">
            <property name="text">
-            <string>Enable Hardware Renderer Fixes</string>
+            <string>Manual Hardware Renderer Fixes</string>
            </property>
           </widget>
          </item>
@@ -661,10 +661,10 @@
        <item row="1" column="1">
         <layout class="QHBoxLayout" name="horizontalLayout">
          <item>
-          <widget class="QSpinBox" name="skipDrawRangeStart"/>
+          <widget class="QSpinBox" name="skipDrawStart"/>
          </item>
          <item>
-          <widget class="QSpinBox" name="skipDrawRangeCount"/>
+          <widget class="QSpinBox" name="skipDrawEnd"/>
          </item>
         </layout>
        </item>
diff --git a/pcsx2/Config.h b/pcsx2/Config.h
index 0cb52ac849..9b96b663ba 100644
--- a/pcsx2/Config.h
+++ b/pcsx2/Config.h
@@ -442,7 +442,7 @@ struct Pcsx2Config
 					WrapGSMem : 1,
 					Mipmap : 1,
 					AA1 : 1,
-					UserHacks : 1,
+					ManualUserHacks : 1,
 					UserHacks_AlignSpriteX : 1,
 					UserHacks_AutoFlush : 1,
 					UserHacks_CPUFBConversion : 1,
@@ -510,8 +510,8 @@ struct Pcsx2Config
 		int SWExtraThreads{2};
 		int SWExtraThreadsHeight{4};
 		int TVShader{0};
-		int SkipDraw{0};
-		int SkipDrawOffset{0};
+		int SkipDrawStart{0};
+		int SkipDrawEnd{0};
 
 		int UserHacks_HalfBottomOverride{-1};
 		int UserHacks_HalfPixelOffset{0};
diff --git a/pcsx2/GS/GS.cpp b/pcsx2/GS/GS.cpp
index 0978412c68..c29670a4ff 100644
--- a/pcsx2/GS/GS.cpp
+++ b/pcsx2/GS/GS.cpp
@@ -310,8 +310,6 @@ bool GSopen(const Pcsx2Config::GSOptions& config, GSRendererType renderer, u8* b
 
 	GSConfig = config;
 	GSConfig.Renderer = renderer;
-	GSConfig.MaskUserHacks();
-	GSConfig.MaskUpscalingHacks();
 
 	if (!Host::AcquireHostDisplay(GetAPIForRenderer(renderer)))
 	{
@@ -724,8 +722,6 @@ void GSUpdateConfig(const Pcsx2Config::GSOptions& new_config)
 	Pcsx2Config::GSOptions old_config(std::move(GSConfig));
 	GSConfig = new_config;
 	GSConfig.Renderer = (GSConfig.Renderer == GSRendererType::Auto) ? GSUtil::GetPreferredRenderer() : GSConfig.Renderer;
-	GSConfig.MaskUserHacks();
-	GSConfig.MaskUpscalingHacks();
 	if (!s_gs)
 		return;
 
diff --git a/pcsx2/GS/Renderers/HW/GSHwHack.cpp b/pcsx2/GS/Renderers/HW/GSHwHack.cpp
index 3eedce61bc..1c0d300833 100644
--- a/pcsx2/GS/Renderers/HW/GSHwHack.cpp
+++ b/pcsx2/GS/Renderers/HW/GSHwHack.cpp
@@ -1053,7 +1053,7 @@ bool GSState::IsBadFrame()
 		return false;
 	}
 
-	if (m_skip == 0 && GSConfig.SkipDraw > 0)
+	if (m_skip == 0 && GSConfig.SkipDrawEnd > 0)
 	{
 		if (fi.TME)
 		{
@@ -1061,8 +1061,8 @@ bool GSState::IsBadFrame()
 			// General, often problematic post processing
 			if (GSLocalMemory::m_psm[fi.TPSM].depth || GSUtil::HasSharedBits(fi.FBP, fi.FPSM, fi.TBP0, fi.TPSM))
 			{
-				m_skip_offset = GSConfig.SkipDrawOffset;
-				m_skip = std::max(GSConfig.SkipDraw, m_skip_offset);
+				m_skip_offset = GSConfig.SkipDrawStart;
+				m_skip = GSConfig.SkipDrawEnd;
 			}
 		}
 	}
diff --git a/pcsx2/GS/Window/GSwxDialog.cpp b/pcsx2/GS/Window/GSwxDialog.cpp
index 55287b0848..3f3a04a175 100644
--- a/pcsx2/GS/Window/GSwxDialog.cpp
+++ b/pcsx2/GS/Window/GSwxDialog.cpp
@@ -328,7 +328,7 @@ HacksTab::HacksTab(wxWindow* parent)
 	PaddedBoxSizer<wxBoxSizer> tab_box(wxVERTICAL);
 
 	auto hw_prereq = [this]{ return m_is_hardware; };
-	auto* hacks_check_box = m_ui.addCheckBox(tab_box.inner, "Enable HW Hacks", "UserHacks", -1, hw_prereq);
+	auto* hacks_check_box = m_ui.addCheckBox(tab_box.inner, "Manual HW Hacks", "UserHacks", -1, hw_prereq);
 	auto hacks_prereq = [this, hacks_check_box]{ return m_is_hardware && hacks_check_box->GetValue(); };
 	auto upscale_hacks_prereq = [this, hacks_check_box]{ return !m_is_native_res && hacks_check_box->GetValue(); };
 
diff --git a/pcsx2/GameDatabase.cpp b/pcsx2/GameDatabase.cpp
index 6559bd451b..8a7461d232 100644
--- a/pcsx2/GameDatabase.cpp
+++ b/pcsx2/GameDatabase.cpp
@@ -16,8 +16,8 @@
 #include "PrecompiledHeader.h"
 
 #include "GameDatabase.h"
-#include "Config.h"
 #include "Host.h"
+#include "Patch.h"
 
 #include "common/FileSystem.h"
 #include "common/Path.h"
@@ -31,6 +31,20 @@
 #include "fmt/ranges.h"
 #include <fstream>
 #include <mutex>
+#include <optional>
+
+namespace GameDatabaseSchema
+{
+	static const char* getHWFixName(GSHWFixId id);
+	static std::optional<GSHWFixId> parseHWFixName(const std::string_view& name);
+	static bool isUserHackHWFix(GSHWFixId id);
+} // namespace GameDatabaseSchema
+
+namespace GameDatabase
+{
+	static void parseAndInsert(const std::string_view& serial, const c4::yml::NodeRef& node);
+	static void initDatabase();
+} // namespace GameDatabase
 
 static constexpr char GAMEDB_YAML_FILE_NAME[] = "GameIndex.yaml";
 
@@ -85,7 +99,7 @@ const char* GameDatabaseSchema::GameEntry::compatAsString() const
 	}
 }
 
-void parseAndInsert(const std::string_view& serial, const c4::yml::NodeRef& node)
+void GameDatabase::parseAndInsert(const std::string_view& serial, const c4::yml::NodeRef& node)
 {
 	GameDatabaseSchema::GameEntry gameEntry;
 	if (node.has_child("name"))
@@ -195,6 +209,25 @@ void parseAndInsert(const std::string_view& serial, const c4::yml::NodeRef& node
 		}
 	}
 
+	if (node.has_child("gsHWFixes"))
+	{
+		for (const ryml::NodeRef& n : node["gsHWFixes"].children())
+		{
+			const std::string_view id_name(n.key().data(), n.key().size());
+			std::optional<GameDatabaseSchema::GSHWFixId> id = GameDatabaseSchema::parseHWFixName(id_name);
+			std::optional<s32> value = n.has_val() ? StringUtil::FromChars<s32>(std::string_view(n.val().data(), n.val().size())) : 1;
+			if (!id.has_value() || !value.has_value())
+			{
+				Console.Error("[GameDB] Invalid GS HW Fix: '%*s' specified for serial '%*s'. Dropping!",
+					static_cast<int>(id_name.size()), id_name.data(),
+					static_cast<int>(serial.size()), serial.data());
+				continue;
+			}
+
+			gameEntry.gsHWFixes.emplace_back(id.value(), value.value());
+		}
+	}
+
 	// Memory Card Filters - Store as a vector to allow flexibility in the future
 	// - currently they are used as a '\n' delimited string in the app
 	if (node.has_child("memcardFilters") && node["memcardFilters"].has_children())
@@ -231,16 +264,188 @@ void parseAndInsert(const std::string_view& serial, const c4::yml::NodeRef& node
 	s_game_db.emplace(std::move(serial), std::move(gameEntry));
 }
 
-static std::ifstream getFileStream(std::string path)
+static const char* s_gs_hw_fix_names[] = {
+	"autoFlush",
+	"conservativeFramebuffer",
+	"cpuFramebufferConversion",
+	"disableDepthSupport",
+	"wrapGSMem",
+	"preloadFrameData",
+	"fastTextureInvalidation",
+	"textureInsideRT",
+	"alignSprite",
+	"mergeSprite",
+	"wildArmsHack",
+	"mipmap",
+	"trilinearFiltering",
+	"skipDrawStart",
+	"skipDrawEnd",
+	"halfBottomOverride",
+	"halfPixelOffset",
+	"roundSprite",
+	"texturePreloading",
+};
+static_assert(std::size(s_gs_hw_fix_names) == static_cast<u32>(GameDatabaseSchema::GSHWFixId::Count), "HW fix name lookup is correct size");
+
+const char* GameDatabaseSchema::getHWFixName(GSHWFixId id)
 {
-#ifdef _WIN32
-	return std::ifstream(StringUtil::UTF8StringToWideString(path));
-#else
-	return std::ifstream(path.c_str());
-#endif
+	return s_gs_hw_fix_names[static_cast<u32>(id)];
 }
 
-static void initDatabase()
+static std::optional<GameDatabaseSchema::GSHWFixId> GameDatabaseSchema::parseHWFixName(const std::string_view& name)
+{
+	for (u32 i = 0; i < std::size(s_gs_hw_fix_names); i++)
+	{
+		if (name.compare(s_gs_hw_fix_names[i]) == 0)
+			return static_cast<GameDatabaseSchema::GSHWFixId>(i);
+	}
+
+	return std::nullopt;
+}
+
+bool GameDatabaseSchema::isUserHackHWFix(GSHWFixId id)
+{
+	switch (id)
+	{
+		case GSHWFixId::Mipmap:
+		case GSHWFixId::TexturePreloading:
+		case GSHWFixId::ConservativeFramebuffer:
+			return false;
+
+#ifdef PCSX2_CORE
+			// Trifiltering isn't a hack in Qt.
+		case GSHWFixId::TrilinearFiltering:
+			return false;
+#endif
+
+		default:
+			return true;
+	}
+}
+
+u32 GameDatabaseSchema::GameEntry::applyGSHardwareFixes(Pcsx2Config::GSOptions& config) const
+{
+	// Only apply GS HW fixes if the user hasn't manually enabled HW fixes.
+	const bool apply_auto_fixes = !config.ManualUserHacks;
+	if (!apply_auto_fixes)
+		Console.Warning("[GameDB] Hardware fixes are enabled, not using automatic fixes.");
+
+	u32 num_applied_fixes = 0;
+	for (const auto& [id, value] : gsHWFixes)
+	{
+		if (isUserHackHWFix(id) && !apply_auto_fixes)
+		{
+			PatchesCon->Warning("[GameDB] Skipping GS Hardware Fix: %s to [mode=%d]", getHWFixName(id), value);
+			continue;
+		}
+
+		switch (id)
+		{
+			case GSHWFixId::AutoFlush:
+				config.UserHacks_AutoFlush = (value > 0);
+				break;
+
+			case GSHWFixId::ConservativeFramebuffer:
+				config.ConservativeFramebuffer = (value > 0);
+				break;
+
+			case GSHWFixId::CPUFramebufferConversion:
+				config.UserHacks_CPUFBConversion = (value > 0);
+				break;
+
+			case GSHWFixId::DisableDepthSupport:
+				config.UserHacks_DisableDepthSupport = (value > 0);
+				break;
+
+			case GSHWFixId::WrapGSMem:
+				config.WrapGSMem = (value > 0);
+				break;
+
+			case GSHWFixId::PreloadFrameData:
+				config.PreloadFrameWithGSData = (value > 0);
+				break;
+
+			case GSHWFixId::FastTextureInvalidation:
+				config.UserHacks_DisablePartialInvalidation = (value > 0);
+				break;
+
+			case GSHWFixId::TextureInsideRT:
+				config.UserHacks_TextureInsideRt = (value > 0);
+				break;
+
+			case GSHWFixId::AlignSprite:
+				config.UserHacks_AlignSpriteX = (value > 0);
+				break;
+
+			case GSHWFixId::MergeSprite:
+				config.UserHacks_MergePPSprite = (value > 0);
+				break;
+
+			case GSHWFixId::WildArmsHack:
+				config.UserHacks_WildHack = (value > 0);
+				break;
+
+			case GSHWFixId::Mipmap:
+			{
+				if (value >= 0 && value <= static_cast<int>(HWMipmapLevel::Full))
+				{
+					if (config.HWMipmap == HWMipmapLevel::Automatic)
+						config.HWMipmap = static_cast<HWMipmapLevel>(value);
+					else if (config.HWMipmap == HWMipmapLevel::Off)
+						Console.Warning("[GameDB] Game requires mipmapping but it has been force disabled.");
+				}
+			}
+			break;
+
+			case GSHWFixId::TrilinearFiltering:
+			{
+				if (value >= 0 && value <= static_cast<int>(TriFiltering::Forced))
+					config.UserHacks_TriFilter = static_cast<TriFiltering>(value);
+			}
+			break;
+
+			case GSHWFixId::SkipDrawStart:
+				config.SkipDrawStart = value;
+				break;
+
+			case GSHWFixId::SkipDrawEnd:
+				config.SkipDrawEnd = value;
+				break;
+
+			case GSHWFixId::HalfBottomOverride:
+				config.UserHacks_HalfBottomOverride = value;
+				break;
+
+			case GSHWFixId::HalfPixelOffset:
+				config.UserHacks_HalfPixelOffset = value;
+				break;
+
+			case GSHWFixId::RoundSprite:
+				config.UserHacks_RoundSprite = value;
+				break;
+
+			case GSHWFixId::TexturePreloading:
+			{
+				if (value >= 0 && value <= static_cast<int>(TexturePreloadingLevel::Full))
+					config.TexturePreloading = std::min(config.TexturePreloading, static_cast<TexturePreloadingLevel>(value));
+			}
+			break;
+
+			default:
+				break;
+		}
+
+		PatchesCon->WriteLn("[GameDB] Enabled GS Hardware Fix: %s to [mode=%d]", getHWFixName(id), value);
+		num_applied_fixes++;
+	}
+
+	// fixup skipdraw range just in case the db has a bad range (but the linter should catch this)
+	config.SkipDrawEnd = std::max(config.SkipDrawStart, config.SkipDrawEnd);
+
+	return num_applied_fixes;
+}
+
+void GameDatabase::initDatabase()
 {
 	ryml::Callbacks rymlCallbacks = ryml::get_callbacks();
 	rymlCallbacks.m_error = [](const char* msg, size_t msg_len, ryml::Location loc, void*) {
@@ -291,8 +496,6 @@ static void initDatabase()
 	ryml::reset_callbacks();
 }
 
-
-
 void GameDatabase::ensureLoaded()
 {
 	std::call_once(s_load_once_flag, []() {
diff --git a/pcsx2/GameDatabase.h b/pcsx2/GameDatabase.h
index cf6264d1b5..7b6331c06e 100644
--- a/pcsx2/GameDatabase.h
+++ b/pcsx2/GameDatabase.h
@@ -15,16 +15,18 @@
 
 #pragma once
 
+#include "Config.h"
+#include <optional>
+#include <string>
+#include <string_view>
 #include <unordered_map>
 #include <vector>
-#include <string>
 
 enum GamefixId;
 enum SpeedhackId;
 
-class GameDatabaseSchema
+namespace GameDatabaseSchema
 {
-public:
 	enum class Compatibility
 	{
 		Unknown = 0,
@@ -54,6 +56,34 @@ public:
 		Full
 	};
 
+	enum class GSHWFixId : u32
+	{
+		// boolean settings
+		AutoFlush,
+		ConservativeFramebuffer,
+		CPUFramebufferConversion,
+		DisableDepthSupport,
+		WrapGSMem,
+		PreloadFrameData,
+		FastTextureInvalidation,
+		TextureInsideRT,
+		AlignSprite,
+		MergeSprite,
+		WildArmsHack,
+
+		// integer settings
+		Mipmap,
+		TrilinearFiltering,
+		SkipDrawStart,
+		SkipDrawEnd,
+		HalfBottomOverride,
+		HalfPixelOffset,
+		RoundSprite,
+		TexturePreloading,
+
+		Count
+	};
+
 	using Patch = std::vector<std::string>;
 
 	struct GameEntry
@@ -67,6 +97,7 @@ public:
 		ClampMode vuClampMode = ClampMode::Undefined;
 		std::vector<GamefixId> gameFixes;
 		std::vector<std::pair<SpeedhackId, int>> speedHacks;
+		std::vector<std::pair<GSHWFixId, s32>> gsHWFixes;
 		std::vector<std::string> memcardFilters;
 		std::unordered_map<std::string, Patch> patches;
 
@@ -74,6 +105,9 @@ public:
 		std::string memcardFiltersAsString() const;
 		const Patch* findPatch(const std::string_view& crc) const;
 		const char* compatAsString() const;
+
+		/// Applies GS hardware fixes to an existing config. Returns the number of applied fixes.
+		u32 applyGSHardwareFixes(Pcsx2Config::GSOptions& config) const;
 	};
 };
 
diff --git a/pcsx2/Pcsx2Config.cpp b/pcsx2/Pcsx2Config.cpp
index e49a7d1557..6ce60d6224 100644
--- a/pcsx2/Pcsx2Config.cpp
+++ b/pcsx2/Pcsx2Config.cpp
@@ -314,7 +314,7 @@ Pcsx2Config::GSOptions::GSOptions()
 	Mipmap = true;
 	AA1 = true;
 
-	UserHacks = false;
+	ManualUserHacks = false;
 	UserHacks_AlignSpriteX = false;
 	UserHacks_AutoFlush = false;
 	UserHacks_CPUFBConversion = false;
@@ -385,8 +385,8 @@ bool Pcsx2Config::GSOptions::OptionsAreEqual(const GSOptions& right) const
 		OpEqu(SWExtraThreads) &&
 		OpEqu(SWExtraThreadsHeight) &&
 		OpEqu(TVShader) &&
-		OpEqu(SkipDraw) &&
-		OpEqu(SkipDrawOffset) &&
+		OpEqu(SkipDrawEnd) &&
+		OpEqu(SkipDrawStart) &&
 
 		OpEqu(UserHacks_HalfBottomOverride) &&
 		OpEqu(UserHacks_HalfPixelOffset) &&
@@ -513,7 +513,7 @@ void Pcsx2Config::GSOptions::ReloadIniSettings()
 	GSSettingBoolEx(WrapGSMem, "wrap_gs_mem");
 	GSSettingBoolEx(Mipmap, "mipmap");
 	GSSettingBoolEx(AA1, "aa1");
-	GSSettingBoolEx(UserHacks, "UserHacks");
+	GSSettingBoolEx(ManualUserHacks, "UserHacks");
 	GSSettingBoolEx(UserHacks_AlignSpriteX, "UserHacks_align_sprite_X");
 	GSSettingBoolEx(UserHacks_AutoFlush, "UserHacks_AutoFlush");
 	GSSettingBoolEx(UserHacks_CPUFBConversion, "UserHacks_CPU_FB_Conversion");
@@ -555,8 +555,9 @@ void Pcsx2Config::GSOptions::ReloadIniSettings()
 	GSSettingIntEx(SWExtraThreads, "extrathreads");
 	GSSettingIntEx(SWExtraThreadsHeight, "extrathreads_height");
 	GSSettingIntEx(TVShader, "TVShader");
-	GSSettingIntEx(SkipDraw, "UserHacks_SkipDraw");
-	GSSettingIntEx(SkipDrawOffset, "UserHacks_SkipDraw_Offset");
+	GSSettingIntEx(SkipDrawStart, "UserHacks_SkipDraw_Offset");
+	GSSettingIntEx(SkipDrawEnd, "UserHacks_SkipDraw");
+	SkipDrawEnd = std::max(SkipDrawStart, SkipDrawEnd);
 
 	GSSettingIntEx(UserHacks_HalfBottomOverride, "UserHacks_Half_Bottom_Override");
 	GSSettingIntEx(UserHacks_HalfPixelOffset, "UserHacks_HalfPixelOffset");
@@ -588,7 +589,7 @@ void Pcsx2Config::GSOptions::ReloadIniSettings()
 
 void Pcsx2Config::GSOptions::MaskUserHacks()
 {
-	if (UserHacks)
+	if (ManualUserHacks)
 		return;
 
 	UserHacks_AlignSpriteX = false;
@@ -605,8 +606,8 @@ void Pcsx2Config::GSOptions::MaskUserHacks()
 	UserHacks_TextureInsideRt = false;
 	UserHacks_TCOffsetX = 0;
 	UserHacks_TCOffsetY = 0;
-	SkipDraw = 0;
-	SkipDrawOffset = 0;
+	SkipDrawStart = 0;
+	SkipDrawEnd = 0;
 
 	// in wx, we put trilinear filtering behind user hacks, but not in qt.
 #ifndef PCSX2_CORE
@@ -616,7 +617,7 @@ void Pcsx2Config::GSOptions::MaskUserHacks()
 
 void Pcsx2Config::GSOptions::MaskUpscalingHacks()
 {
-	if (UpscaleMultiplier == 1 || UserHacks)
+	if (UpscaleMultiplier == 1 || ManualUserHacks)
 		return;
 
 	UserHacks_AlignSpriteX = false;
diff --git a/pcsx2/VMManager.cpp b/pcsx2/VMManager.cpp
index 40d2228dd2..a3059b68e2 100644
--- a/pcsx2/VMManager.cpp
+++ b/pcsx2/VMManager.cpp
@@ -218,6 +218,10 @@ void VMManager::LoadSettings()
 	InputManager::ReloadSources(*si);
 	InputManager::ReloadBindings(*si);
 
+	// Remove any user-specified hacks in the config (we don't want stale/conflicting values when it's globally disabled).
+	EmuConfig.GS.MaskUserHacks();
+	EmuConfig.GS.MaskUpscalingHacks();
+
 	if (HasValidVM())
 		ApplyGameFixes();
 }
@@ -295,6 +299,8 @@ void VMManager::ApplyGameFixes()
 		if (id == Fix_GoemonTlbMiss && true)
 			vtlb_Alloc_Ppmap();
 	}
+
+	s_active_game_fixes += game->applyGSHardwareFixes(EmuConfig.GS);
 }
 
 std::string VMManager::GetGameSettingsPath(u32 game_crc)
diff --git a/pcsx2/gui/AppCoreThread.cpp b/pcsx2/gui/AppCoreThread.cpp
index 44177e01d1..b27d904e81 100644
--- a/pcsx2/gui/AppCoreThread.cpp
+++ b/pcsx2/gui/AppCoreThread.cpp
@@ -333,6 +333,8 @@ static int loadGameSettings(Pcsx2Config& dest, const GameDatabaseSchema::GameEnt
 			vtlb_Alloc_Ppmap();
 	}
 
+	gf += game.applyGSHardwareFixes(dest.GS);
+
 	return gf;
 }
 
@@ -404,6 +406,10 @@ static void _ApplySettings(const Pcsx2Config& src, Pcsx2Config& fixup)
 		fixup.GS.VsyncEnable = VsyncMode::Off;
 	}
 
+	// Remove any user-specified hacks in the config (we don't want stale/conflicting values when it's globally disabled).
+	fixup.GS.MaskUserHacks();
+	fixup.GS.MaskUpscalingHacks();
+
 	wxString gamePatch;
 	wxString gameFixes;
 	wxString gameCheats;