diff --git a/rpcs3/Emu/System.cpp b/rpcs3/Emu/System.cpp
index e1cdbe36c4..c0de5ebf33 100644
--- a/rpcs3/Emu/System.cpp
+++ b/rpcs3/Emu/System.cpp
@@ -586,7 +586,7 @@ void Emulator::LimitCacheSize()
 	LOG_SUCCESS(GENERAL, "Cleaned disk cache, removed %.2f MB", size / 1024.0 / 1024.0);
 }
 
-bool Emulator::BootGame(const std::string& path, bool direct, bool add_only)
+bool Emulator::BootGame(const std::string& path, bool direct, bool add_only, bool force_global_config)
 {
 	if (g_cfg.vfs.limit_cache_size)
 		LimitCacheSize();
@@ -603,7 +603,7 @@ bool Emulator::BootGame(const std::string& path, bool direct, bool add_only)
 	if (direct && fs::exists(path))
 	{
 		m_path = path;
-		Load(add_only);
+		Load(add_only, force_global_config);
 		return true;
 	}
 
@@ -614,7 +614,7 @@ bool Emulator::BootGame(const std::string& path, bool direct, bool add_only)
 		if (fs::is_file(elf))
 		{
 			m_path = elf;
-			Load(add_only);
+			Load(add_only, force_global_config);
 			return true;
 		}
 	}
@@ -697,12 +697,33 @@ std::string Emulator::GetSfoDirFromGamePath(const std::string& game_path, const
 	return game_path;
 }
 
+std::string Emulator::GetCustomConfigDir()
+{
+#ifdef _WIN32
+	return fs::get_config_dir() + "config/custom_configs/";
+#else
+	return fs::get_config_dir() + "custom_configs/";
+#endif
+}
+
+std::string Emulator::GetCustomConfigPath(const std::string& title_id, bool get_deprecated_path)
+{
+	std::string path;
+
+	if (get_deprecated_path)
+		path = fs::get_config_dir() + "data/" + title_id + "/config.yml";
+	else
+		path = GetCustomConfigDir() + "config_" + title_id + ".yml";
+
+	return path;
+}
+
 void Emulator::SetForceBoot(bool force_boot)
 {
 	m_force_boot = force_boot;
 }
 
-void Emulator::Load(bool add_only)
+void Emulator::Load(bool add_only, bool force_global_config)
 {
 	if (!IsStopped())
 	{
@@ -784,18 +805,31 @@ void Emulator::Load(bool add_only)
 		LOG_NOTICE(LOADER, "Serial: %s", GetTitleID());
 		LOG_NOTICE(LOADER, "Category: %s", GetCat());
 
-		// Load custom config-1
-		if (fs::file cfg_file{fs::get_config_dir() + "data/" + m_title_id + "/config.yml"})
+		if (!force_global_config)
 		{
-			LOG_NOTICE(LOADER, "Applying custom config: data/%s/config.yml", m_title_id);
-			g_cfg.from_string(cfg_file.to_string());
-		}
+			const std::string config_path_new = GetCustomConfigPath(m_title_id);
+			const std::string config_path_old = GetCustomConfigPath(m_title_id, true);
 
-		// Load custom config-2
-		if (fs::file cfg_file{m_path + ".yml"})
-		{
-			LOG_NOTICE(LOADER, "Applying custom config: %s.yml", m_path);
-			g_cfg.from_string(cfg_file.to_string());
+			// Load custom config-1
+			if (fs::file cfg_file{ config_path_old })
+			{
+				LOG_NOTICE(LOADER, "Applying custom config: %s", config_path_old);
+				g_cfg.from_string(cfg_file.to_string());
+			}
+
+			// Load custom config-2
+			if (fs::file cfg_file{ config_path_new })
+			{
+				LOG_NOTICE(LOADER, "Applying custom config: %s", config_path_new);
+				g_cfg.from_string(cfg_file.to_string());
+			}
+
+			// Load custom config-3
+			if (fs::file cfg_file{ m_path + ".yml" })
+			{
+				LOG_NOTICE(LOADER, "Applying custom config: %s.yml", m_path);
+				g_cfg.from_string(cfg_file.to_string());
+			}
 		}
 
 #if defined(_WIN32) || defined(HAVE_VULKAN)
diff --git a/rpcs3/Emu/System.h b/rpcs3/Emu/System.h
index cf09ead762..202d0d0a65 100644
--- a/rpcs3/Emu/System.h
+++ b/rpcs3/Emu/System.h
@@ -309,7 +309,7 @@ public:
 
 	std::string PPUCache() const;
 
-	bool BootGame(const std::string& path, bool direct = false, bool add_only = false);
+	bool BootGame(const std::string& path, bool direct = false, bool add_only = false, bool force_global_config = false);
 	bool BootRsxCapture(const std::string& path);
 	bool InstallPkg(const std::string& path);
 
@@ -322,9 +322,12 @@ public:
 	static std::string GetHddDir();
 	static std::string GetSfoDirFromGamePath(const std::string& game_path, const std::string& user);
 
+	static std::string GetCustomConfigDir();
+	static std::string GetCustomConfigPath(const std::string& title_id, bool get_deprecated_path = false);
+
 	void SetForceBoot(bool force_boot);
 
-	void Load(bool add_only = false);
+	void Load(bool add_only = false, bool force_global_config = false);
 	void Run();
 	bool Pause();
 	void Resume();
diff --git a/rpcs3/rpcs3qt/emu_settings.cpp b/rpcs3/rpcs3qt/emu_settings.cpp
index cb622e9a75..fd5b68fed2 100644
--- a/rpcs3/rpcs3qt/emu_settings.cpp
+++ b/rpcs3/rpcs3qt/emu_settings.cpp
@@ -185,12 +185,12 @@ emu_settings::~emu_settings()
 {
 }
 
-void emu_settings::LoadSettings(const std::string& path)
+void emu_settings::LoadSettings(const std::string& title_id)
 {
-	m_path = path;
+	m_title_id = title_id;
 
 	// Create config path if necessary
-	fs::create_path(fs::get_config_dir() + path);
+	fs::create_path(title_id.empty() ? fs::get_config_dir() : Emu.GetCustomConfigDir());
 
 	// Load default config
 	m_defaultSettings = YAML::Load(g_cfg_defaults);
@@ -202,11 +202,23 @@ void emu_settings::LoadSettings(const std::string& path)
 	config.close();
 
 	// Add game config
-	if (!path.empty() && fs::is_file(fs::get_config_dir() + path + "/config.yml"))
+	if (!title_id.empty())
 	{
-		config = fs::file(fs::get_config_dir() + path + "/config.yml", fs::read + fs::write);
-		m_currentSettings += YAML::Load(config.to_string());
-		config.close();
+		const std::string config_path_new = Emu.GetCustomConfigPath(m_title_id);
+		const std::string config_path_old = Emu.GetCustomConfigPath(m_title_id, true);
+
+		if (fs::is_file(config_path_new))
+		{
+			config = fs::file(config_path_new, fs::read + fs::write);
+			m_currentSettings += YAML::Load(config.to_string());
+			config.close();
+		}
+		else if (fs::is_file(config_path_old))
+		{
+			config = fs::file(config_path_old, fs::read + fs::write);
+			m_currentSettings += YAML::Load(config.to_string());
+			config.close();
+		}
 	}
 }
 
@@ -216,9 +228,9 @@ void emu_settings::SaveSettings()
 	YAML::Emitter out;
 	emitData(out, m_currentSettings);
 
-	if (!m_path.empty())
+	if (!m_title_id.empty())
 	{
-		config = fs::file(fs::get_config_dir() + m_path + "/config.yml", fs::read + fs::write + fs::create);
+		config = fs::file(Emu.GetCustomConfigPath(m_title_id), fs::read + fs::write + fs::create);
 	}
 	else
 	{
diff --git a/rpcs3/rpcs3qt/emu_settings.h b/rpcs3/rpcs3qt/emu_settings.h
index 821628c3ff..82303518bb 100644
--- a/rpcs3/rpcs3qt/emu_settings.h
+++ b/rpcs3/rpcs3qt/emu_settings.h
@@ -1,4 +1,4 @@
-#pragma once
+#pragma once
 
 #include "Utilities/File.h"
 #include "Utilities/Log.h"
@@ -223,7 +223,7 @@ public:
 	Render_Creator m_render_creator;
 
 	/** Loads the settings from path.*/
-	void LoadSettings(const std::string& path = "");
+	void LoadSettings(const std::string& title_id = "");
 
 	/** Fixes all registered invalid settings after asking the user for permission.*/
 	void OpenCorrectionDialog(QWidget* parent = Q_NULLPTR);
@@ -355,5 +355,5 @@ private:
 
 	YAML::Node m_defaultSettings; // The default settings as a YAML node.
 	YAML::Node m_currentSettings; // The current settings as a YAML node.
-	std::string m_path;
+	std::string m_title_id;
 };
diff --git a/rpcs3/rpcs3qt/game_list_frame.cpp b/rpcs3/rpcs3qt/game_list_frame.cpp
index ea3c581957..dbf6bed528 100644
--- a/rpcs3/rpcs3qt/game_list_frame.cpp
+++ b/rpcs3/rpcs3qt/game_list_frame.cpp
@@ -1,4 +1,4 @@
-#include "game_list_frame.h"
+#include "game_list_frame.h"
 #include "qt_utils.h"
 #include "settings_dialog.h"
 #include "table_item_delegate.h"
@@ -461,7 +461,7 @@ void game_list_frame::Refresh(const bool fromDrive, const bool scrollAfter)
 			}
 
 			const auto compat = m_game_compat->GetCompatibility(game.serial);
-			const bool hasCustomConfig = fs::is_file(fs::get_config_dir() + "data/" + game.serial + "/config.yml");
+			const bool hasCustomConfig = fs::is_file(Emu.GetCustomConfigPath(game.serial)) || fs::is_file(Emu.GetCustomConfigPath(game.serial, true));
 			const QColor color = getGridCompatibilityColor(compat.color);
 
 			const QPixmap pxmap = PaintedPixmap(img, hasCustomConfig, color);
@@ -655,12 +655,29 @@ void game_list_frame::ShowContextMenu(const QPoint &pos)
 	const QString serial = qstr(currGame.serial);
 	const QString name = qstr(currGame.name).simplified();
 
+	const std::string cache_base_dir = fs::get_cache_dir() + "cache/" + currGame.serial;
+	const std::string data_base_dir  = fs::get_config_dir() + "data/" + currGame.serial;
+
 	// Make Actions
 	QMenu myMenu;
-	QAction* boot = myMenu.addAction(tr("&Boot"));
+	QAction* boot = new QAction(gameinfo->hasCustomConfig ? tr("&Boot with global configuration") : tr("&Boot"));
 	QFont f = boot->font();
 	f.setBold(true);
-	boot->setFont(f);
+	if (gameinfo->hasCustomConfig)
+	{
+		QAction* boot_custom = myMenu.addAction(tr("&Boot with custom configuration"));
+		boot_custom->setFont(f);
+		connect(boot_custom, &QAction::triggered, [=]
+		{
+			LOG_NOTICE(LOADER, "Booting from gamelist per context menu...");
+			Q_EMIT RequestBoot(currGame.path);
+		});
+	}
+	else
+	{
+		boot->setFont(f);
+	}
+	myMenu.addAction(boot);
 	QAction* configure = myMenu.addAction(tr("&Configure"));
 	QAction* createPPUCache = myMenu.addAction(tr("&Create PPU Cache"));
 	myMenu.addSeparator();
@@ -671,13 +688,57 @@ void game_list_frame::ShowContextMenu(const QPoint &pos)
 	myMenu.addSeparator();
 	QMenu* remove_menu = myMenu.addMenu(tr("&Remove"));
 	QAction* removeGame = remove_menu->addAction(tr("&Remove %1").arg(qstr(currGame.category)));
-	QAction* removeConfig = remove_menu->addAction(tr("&Remove Custom Configuration"));
-	QAction* removeShadersCache = remove_menu->addAction(tr("&Remove Shaders Cache"));
-	QAction* removePPUCache = remove_menu->addAction(tr("&Remove PPU Cache"));
-	QAction* removeSPUCache = remove_menu->addAction(tr("&Remove SPU Cache"));
+	if (gameinfo->hasCustomConfig)
+	{
+		QAction* remove_custom_config = remove_menu->addAction(tr("&Remove Custom Configuration"));
+		connect(remove_custom_config, &QAction::triggered, [=]()
+		{
+			if (RemoveCustomConfiguration(currGame.serial, true))
+			{
+				ShowCustomConfigIcon(item, false);
+			}
+		});
+	}
+	if (fs::is_dir(cache_base_dir))
+	{
+		QAction* removeShadersCache = remove_menu->addAction(tr("&Remove Shaders Cache"));
+		connect(removeShadersCache, &QAction::triggered, [=]()
+		{
+			RemoveShadersCache(cache_base_dir, true);
+		});
+		QAction* removePPUCache = remove_menu->addAction(tr("&Remove PPU Cache"));
+		connect(removePPUCache, &QAction::triggered, [=]()
+		{
+			RemovePPUCache(cache_base_dir, true);
+		});
+		QAction* removeSPUCache = remove_menu->addAction(tr("&Remove SPU Cache"));
+		connect(removeSPUCache, &QAction::triggered, [=]()
+		{
+			RemoveSPUCache(cache_base_dir, true);
+		});
+	}
 	myMenu.addSeparator();
 	QAction* openGameFolder = myMenu.addAction(tr("&Open Install Folder"));
-	QAction* openConfig = myMenu.addAction(tr("&Open Config Folder"));
+	if (gameinfo->hasCustomConfig)
+	{
+		QAction* open_config_dir = myMenu.addAction(tr("&Open Custom Config Folder"));
+		connect(open_config_dir, &QAction::triggered, [=]()
+		{
+			if (fs::is_file(Emu.GetCustomConfigPath(currGame.serial, true)))
+				open_dir(Emu.GetCustomConfigDir());
+
+			if (fs::is_file(Emu.GetCustomConfigPath(currGame.serial)))
+				open_dir(data_base_dir);
+		});
+	}
+	if (fs::is_dir(data_base_dir))
+	{
+		QAction* open_data_dir = myMenu.addAction(tr("&Open Data Folder"));
+		connect(open_data_dir, &QAction::triggered, [=]()
+		{
+			open_dir(data_base_dir);
+		});
+	}
 	myMenu.addSeparator();
 	QAction* checkCompat = myMenu.addAction(tr("&Check Game Compatibility"));
 	QAction* downloadCompat = myMenu.addAction(tr("&Download Compatibility Database"));
@@ -688,13 +749,10 @@ void game_list_frame::ShowContextMenu(const QPoint &pos)
 	QAction* copy_name = info_menu->addAction(tr("&Copy Name"));
 	QAction* copy_serial = info_menu->addAction(tr("&Copy Serial"));
 
-	const std::string cache_base_dir = fs::get_cache_dir() + "cache/" + currGame.serial;
-	const std::string config_base_dir = fs::get_config_dir() + "data/" + currGame.serial;
-
 	connect(boot, &QAction::triggered, [=]
 	{
 		LOG_NOTICE(LOADER, "Booting from gamelist per context menu...");
-		Q_EMIT RequestBoot(currGame.path);
+		Q_EMIT RequestBoot(currGame.path, gameinfo->hasCustomConfig);
 	});
 	connect(configure, &QAction::triggered, [=]
 	{
@@ -739,7 +797,7 @@ void game_list_frame::ShowContextMenu(const QPoint &pos)
 				RemoveShadersCache(cache_base_dir);
 				RemovePPUCache(cache_base_dir);
 				RemoveSPUCache(cache_base_dir);
-				RemoveCustomConfiguration(config_base_dir);
+				RemoveCustomConfiguration(currGame.serial);
 			}
 			fs::remove_all(currGame.path);
 			m_game_data.erase(std::remove(m_game_data.begin(), m_game_data.end(), gameinfo), m_game_data.end());
@@ -754,33 +812,10 @@ void game_list_frame::ShowContextMenu(const QPoint &pos)
 			LOG_SUCCESS(GENERAL, "Removed %s %s in %s", currGame.category, currGame.name, currGame.path);
 		}
 	});
-	connect(removeConfig, &QAction::triggered, [=]()
-	{
-		if (RemoveCustomConfiguration(config_base_dir, true))
-		{
-			ShowCustomConfigIcon(item, false);
-		}
-	});
-	connect(removeShadersCache, &QAction::triggered, [=]()
-	{
-		RemoveShadersCache(cache_base_dir, true);
-	});
-	connect(removePPUCache, &QAction::triggered, [=]()
-	{
-		RemovePPUCache(cache_base_dir, true);
-	});
-	connect(removeSPUCache, &QAction::triggered, [=]()
-	{
-		RemoveSPUCache(cache_base_dir, true);
-	});
 	connect(openGameFolder, &QAction::triggered, [=]()
 	{
 		open_dir(currGame.path);
 	});
-	connect(openConfig, &QAction::triggered, [=]()
-	{
-		open_dir(fs::get_config_dir() + "data/" + currGame.serial);
-	});
 	connect(checkCompat, &QAction::triggered, [=]
 	{
 		QString link = "https://rpcs3.net/compatibility?g=" + serial;
@@ -852,61 +887,57 @@ void game_list_frame::ShowContextMenu(const QPoint &pos)
 		QApplication::clipboard()->setText(serial);
 	});
 
-	//Disable options depending on software category
+	// Disable options depending on software category
 	QString category = qstr(currGame.category);
 
 	if (category == category::disc_game)
 	{
 		removeGame->setEnabled(false);
 	}
-	else if (0)
-	{
-		boot->setEnabled(false), f.setBold(false), boot->setFont(f);
-		configure->setEnabled(false);
-		removeConfig->setEnabled(false);
-		openConfig->setEnabled(false);
-		checkCompat->setEnabled(false);
-	}
 	else if (category != category::hdd_game)
 	{
 		checkCompat->setEnabled(false);
 	}
 
-	// Disable removeconfig if no config exists.
-	removeConfig->setEnabled(gameinfo->hasCustomConfig);
-
-	// remove options if necessary
-	if (!fs::is_dir(cache_base_dir))
-	{
-		removeShadersCache->setEnabled(false);
-		removePPUCache->setEnabled(false);
-		removeSPUCache->setEnabled(false);
-	}
-
 	myMenu.exec(globalPos);
 }
 
-bool game_list_frame::RemoveCustomConfiguration(const std::string& base_dir, bool is_interactive)
+bool game_list_frame::RemoveCustomConfiguration(const std::string& title_id, bool is_interactive)
 {
-	const std::string config_path = base_dir + "/config.yml";
+	const std::string config_path_new = Emu.GetCustomConfigPath(title_id);
+	const std::string config_path_old = Emu.GetCustomConfigPath(title_id, true);
 
-	if (!fs::is_file(config_path))
+	if (!fs::is_file(config_path_new) && !fs::is_file(config_path_old))
 		return false;
 
 	if (is_interactive && QMessageBox::question(this, tr("Confirm Removal"), tr("Remove custom game configuration?")) != QMessageBox::Yes)
 		return false;
 
-	if (fs::remove_file(config_path))
+	bool result = true;
+
+	for (const std::string& path : { config_path_new, config_path_old })
 	{
-		LOG_SUCCESS(GENERAL, "Removed configuration file: %s", config_path);
-		return true;
+		if (!fs::is_file(path))
+		{
+			continue;
+		}
+		if (fs::remove_file(path))
+		{
+			LOG_SUCCESS(GENERAL, "Removed configuration file: %s", path);
+		}
+		else
+		{
+			LOG_FATAL(GENERAL, "Failed to remove configuration file: %s\nError: %s", path, fs::g_tls_error);
+			result = false;
+		}
 	}
-	else
+
+	if (is_interactive && !result)
 	{
 		QMessageBox::warning(this, tr("Warning!"), tr("Failed to remove configuration file!"));
-		LOG_FATAL(GENERAL, "Failed to remove configuration file: %s\nError: %s", config_path, fs::g_tls_error);
-		return false;
 	}
+
+	return result;
 }
 
 bool game_list_frame::RemoveShadersCache(const std::string& base_dir, bool is_interactive)
diff --git a/rpcs3/rpcs3qt/game_list_frame.h b/rpcs3/rpcs3qt/game_list_frame.h
index 7377a99ddd..ee99d6825b 100644
--- a/rpcs3/rpcs3qt/game_list_frame.h
+++ b/rpcs3/rpcs3qt/game_list_frame.h
@@ -1,4 +1,4 @@
-#pragma once
+#pragma once
 
 #include "stdafx.h"
 #include "Emu/GameInfo.h"
@@ -225,7 +225,7 @@ private Q_SLOTS:
 	void doubleClickedSlot(QTableWidgetItem *item);
 Q_SIGNALS:
 	void GameListFrameClosed();
-	void RequestBoot(const std::string& path);
+	void RequestBoot(const std::string& path, bool force_global_config = false);
 	void RequestIconSizeChange(const int& val);
 protected:
 	/** Override inherited method from Qt to allow signalling when close happened.*/
diff --git a/rpcs3/rpcs3qt/main_window.cpp b/rpcs3/rpcs3qt/main_window.cpp
index 9d5e2a62b8..d769be9ff0 100644
--- a/rpcs3/rpcs3qt/main_window.cpp
+++ b/rpcs3/rpcs3qt/main_window.cpp
@@ -268,7 +268,7 @@ void main_window::OnPlayOrPause()
 	}
 }
 
-void main_window::Boot(const std::string& path, bool direct, bool add_only)
+void main_window::Boot(const std::string& path, bool direct, bool add_only, bool force_global_config)
 {
 	if (!Emu.IsStopped())
 	{
@@ -287,7 +287,7 @@ void main_window::Boot(const std::string& path, bool direct, bool add_only)
 	Emu.SetForceBoot(true);
 	Emu.Stop();
 
-	if (Emu.BootGame(path, direct, add_only))
+	if (Emu.BootGame(path, direct, add_only, force_global_config))
 	{
 		LOG_SUCCESS(LOADER, "Boot successful.");
 		const std::string serial = Emu.GetTitleID().empty() ? "" : "[" + Emu.GetTitleID() + "] ";
@@ -1565,7 +1565,10 @@ void main_window::CreateDockWindows()
 		}
 	});
 
-	connect(m_gameListFrame, &game_list_frame::RequestBoot, [this](const std::string& path){ Boot(path); });
+	connect(m_gameListFrame, &game_list_frame::RequestBoot, [this](const std::string& path, bool force_global_config)
+	{
+		Boot(path, false, false, force_global_config);
+	});
 }
 
 void main_window::ConfigureGuiFromSettings(bool configure_all)
diff --git a/rpcs3/rpcs3qt/main_window.h b/rpcs3/rpcs3qt/main_window.h
index 91eb25900a..2e39786cba 100644
--- a/rpcs3/rpcs3qt/main_window.h
+++ b/rpcs3/rpcs3qt/main_window.h
@@ -89,7 +89,7 @@ public Q_SLOTS:
 
 private Q_SLOTS:
 	void OnPlayOrPause();
-	void Boot(const std::string& path, bool direct = false, bool add_only = false);
+	void Boot(const std::string& path, bool direct = false, bool add_only = false, bool force_global_config = false);
 	void BootElf();
 	void BootGame();
 	void BootRsxCapture(std::string path = "");
diff --git a/rpcs3/rpcs3qt/settings_dialog.cpp b/rpcs3/rpcs3qt/settings_dialog.cpp
index 894ae17320..df23cb743d 100644
--- a/rpcs3/rpcs3qt/settings_dialog.cpp
+++ b/rpcs3/rpcs3qt/settings_dialog.cpp
@@ -1,4 +1,4 @@
-#include <QVBoxLayout>
+#include <QVBoxLayout>
 #include <QButtonGroup>
 #include <QPushButton>
 #include <QMessageBox>
@@ -99,7 +99,7 @@ settings_dialog::settings_dialog(std::shared_ptr<gui_settings> guiSettings, std:
 
 	if (game)
 	{
-		xemu_settings->LoadSettings("data/" + game->serial);
+		xemu_settings->LoadSettings(game->serial);
 		setWindowTitle(tr("Settings: [") + qstr(game->serial) + "] " + qstr(game->name));
 	}
 	else