diff --git a/Source/Core/DolphinWX/Debugger/BreakpointWindow.cpp b/Source/Core/DolphinWX/Debugger/BreakpointWindow.cpp
index 1649991d44..4e22b8fbdf 100644
--- a/Source/Core/DolphinWX/Debugger/BreakpointWindow.cpp
+++ b/Source/Core/DolphinWX/Debugger/BreakpointWindow.cpp
@@ -19,6 +19,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
+#include "Core/ConfigManager.h"
 #include "Core/HW/Memmap.h"
 #include "Core/PowerPC/PowerPC.h"
 #include "DolphinWX/WxUtils.h"
@@ -66,7 +67,7 @@ public:
 		}
 
 		AddTool(ID_LOAD, _("Load"), m_Bitmaps[Toolbar_Delete]);
-		Bind(wxEVT_TOOL, &CBreakPointWindow::LoadAll, parent, ID_LOAD);
+		Bind(wxEVT_TOOL, &CBreakPointWindow::Event_LoadAll, parent, ID_LOAD);
 
 		AddTool(ID_SAVE, _("Save"), m_Bitmaps[Toolbar_Delete]);
 		Bind(wxEVT_TOOL, &CBreakPointWindow::Event_SaveAll, parent, ID_SAVE);
@@ -180,32 +181,38 @@ void CBreakPointWindow::SaveAll()
 {
 	// simply dump all to bp/mc files in a way we can read again
 	IniFile ini;
-	if (ini.Load(File::GetUserPath(F_DEBUGGERCONFIG_IDX)))
-	{
-		ini.SetLines("BreakPoints", PowerPC::breakpoints.GetStrings());
-		ini.SetLines("MemoryChecks", PowerPC::memchecks.GetStrings());
-		ini.Save(File::GetUserPath(F_DEBUGGERCONFIG_IDX));
-	}
+	ini.Load(File::GetUserPath(D_GAMESETTINGS_IDX) + SConfig::GetInstance().m_LocalCoreStartupParameter.GetUniqueID() + ".ini", false);
+	ini.SetLines("BreakPoints", PowerPC::breakpoints.GetStrings());
+	ini.SetLines("MemoryChecks", PowerPC::memchecks.GetStrings());
+	ini.Save(File::GetUserPath(D_GAMESETTINGS_IDX) + SConfig::GetInstance().m_LocalCoreStartupParameter.GetUniqueID() + ".ini");
 }
 
-void CBreakPointWindow::LoadAll(wxCommandEvent& WXUNUSED(event))
+void CBreakPointWindow::Event_LoadAll(wxCommandEvent& WXUNUSED(event))
+{
+	LoadAll();
+	return;
+}
+
+void CBreakPointWindow::LoadAll()
 {
 	IniFile ini;
 	BreakPoints::TBreakPointsStr newbps;
 	MemChecks::TMemChecksStr newmcs;
 
-	if (!ini.Load(File::GetUserPath(F_DEBUGGERCONFIG_IDX)))
+	if (!ini.Load(File::GetUserPath(D_GAMESETTINGS_IDX) + SConfig::GetInstance().m_LocalCoreStartupParameter.GetUniqueID() + ".ini", false))
 	{
 		return;
 	}
 
 	if (ini.GetLines("BreakPoints", &newbps, false))
 	{
+		PowerPC::breakpoints.Clear();
 		PowerPC::breakpoints.AddFromStrings(newbps);
 	}
 
 	if (ini.GetLines("MemoryChecks", &newmcs, false))
 	{
+		PowerPC::memchecks.Clear();
 		PowerPC::memchecks.AddFromStrings(newmcs);
 	}
 
diff --git a/Source/Core/DolphinWX/Debugger/BreakpointWindow.h b/Source/Core/DolphinWX/Debugger/BreakpointWindow.h
index 8c2ffc9a2b..03549a241c 100644
--- a/Source/Core/DolphinWX/Debugger/BreakpointWindow.h
+++ b/Source/Core/DolphinWX/Debugger/BreakpointWindow.h
@@ -39,7 +39,8 @@ public:
 	void OnAddMemoryCheck(wxCommandEvent& WXUNUSED(event));
 	void Event_SaveAll(wxCommandEvent& WXUNUSED(event));
 	void SaveAll();
-	void LoadAll(wxCommandEvent& WXUNUSED(event));
+	void Event_LoadAll(wxCommandEvent& WXUNUSED(event));
+	void LoadAll();
 
 private:
 	DECLARE_EVENT_TABLE();
diff --git a/Source/Core/DolphinWX/Debugger/WatchWindow.cpp b/Source/Core/DolphinWX/Debugger/WatchWindow.cpp
index dc25d32d4b..ef192b7419 100644
--- a/Source/Core/DolphinWX/Debugger/WatchWindow.cpp
+++ b/Source/Core/DolphinWX/Debugger/WatchWindow.cpp
@@ -16,6 +16,7 @@
 
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
+#include "Core/ConfigManager.h"
 #include "Core/PowerPC/PowerPC.h"
 #include "DolphinWX/WxUtils.h"
 #include "DolphinWX/Debugger/WatchView.h"
@@ -44,7 +45,7 @@ CWatchToolbar(CWatchWindow* parent, const wxWindowID id)
 	m_Bitmaps[Toolbar_File] = wxBitmap(wxGetBitmapFromMemory(toolbar_delete_png).ConvertToImage().Rescale(16, 16));
 
 	AddTool(ID_LOAD, _("Load"), m_Bitmaps[Toolbar_File]);
-	Bind(wxEVT_TOOL, &CWatchWindow::LoadAll, parent, ID_LOAD);
+	Bind(wxEVT_TOOL, &CWatchWindow::Event_LoadAll, parent, ID_LOAD);
 
 	AddTool(ID_SAVE, _("Save"), m_Bitmaps[Toolbar_File]);
 	Bind(wxEVT_TOOL, &CWatchWindow::Event_SaveAll, parent, ID_SAVE);
@@ -87,6 +88,11 @@ CWatchWindow::CWatchWindow(wxWindow* parent, wxWindowID id,
 	m_mgr.Update();
 }
 
+CWatchWindow::~CWatchWindow()
+{
+	m_mgr.UnInit();
+}
+
 void CWatchWindow::NotifyUpdate()
 {
 	if (m_GPRGridView != nullptr)
@@ -101,25 +107,29 @@ void CWatchWindow::Event_SaveAll(wxCommandEvent& WXUNUSED(event))
 void CWatchWindow::SaveAll()
 {
 	IniFile ini;
-	if (ini.Load(File::GetUserPath(F_DEBUGGERCONFIG_IDX)))
-	{
-		ini.SetLines("Watches", PowerPC::watches.GetStrings());
-		ini.Save(File::GetUserPath(F_DEBUGGERCONFIG_IDX));
-	}
+	ini.Load(File::GetUserPath(D_GAMESETTINGS_IDX) + SConfig::GetInstance().m_LocalCoreStartupParameter.GetUniqueID() + ".ini", false);
+	ini.SetLines("Watches", PowerPC::watches.GetStrings());
+	ini.Save(File::GetUserPath(D_GAMESETTINGS_IDX) + SConfig::GetInstance().m_LocalCoreStartupParameter.GetUniqueID() + ".ini");
 }
 
-void CWatchWindow::LoadAll(wxCommandEvent& WXUNUSED(event))
+void CWatchWindow::Event_LoadAll(wxCommandEvent& WXUNUSED(event))
+{
+	LoadAll();
+}
+
+void CWatchWindow::LoadAll()
 {
 	IniFile ini;
 	Watches::TWatchesStr watches;
 
-	if (!ini.Load(File::GetUserPath(F_DEBUGGERCONFIG_IDX)))
+	if (!ini.Load(File::GetUserPath(D_GAMESETTINGS_IDX) + SConfig::GetInstance().m_LocalCoreStartupParameter.GetUniqueID() + ".ini", false))
 	{
 		return;
 	}
 
 	if (ini.GetLines("Watches", &watches, false))
 	{
+		PowerPC::watches.Clear();
 		PowerPC::watches.AddFromStrings(watches);
 	}
 
diff --git a/Source/Core/DolphinWX/Debugger/WatchWindow.h b/Source/Core/DolphinWX/Debugger/WatchWindow.h
index 2f7dd75839..360974dcb3 100644
--- a/Source/Core/DolphinWX/Debugger/WatchWindow.h
+++ b/Source/Core/DolphinWX/Debugger/WatchWindow.h
@@ -26,11 +26,13 @@ public:
 			const wxSize& size = wxDefaultSize,
 			long style = wxTAB_TRAVERSAL | wxNO_BORDER,
 			const wxString& name = _("Watch"));
+	~CWatchWindow();
 
 	void NotifyUpdate();
 	void Event_SaveAll(wxCommandEvent& WXUNUSED(event));
 	void SaveAll();
-	void LoadAll(wxCommandEvent& WXUNUSED(event));
+	void Event_LoadAll(wxCommandEvent& WXUNUSED(event));
+	void LoadAll();
 
 private:
 	DECLARE_EVENT_TABLE();
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index eb9c6632a7..2ef29ccecc 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -78,7 +78,9 @@
 #include "DolphinWX/WXInputBase.h"
 #include "DolphinWX/WxUtils.h"
 #include "DolphinWX/Cheats/CheatsWindow.h"
+#include "DolphinWX/Debugger/BreakpointWindow.h"
 #include "DolphinWX/Debugger/CodeWindow.h"
+#include "DolphinWX/Debugger/WatchWindow.h"
 
 #include "InputCommon/ControllerInterface/ControllerInterface.h"
 
@@ -656,7 +658,19 @@ void CFrame::BootGame(const std::string& filename)
 		}
 	}
 	if (!bootfile.empty())
+	{
 		StartGame(bootfile);
+		if (UseDebugger)
+		{
+			if (g_pCodeWindow)
+			{
+				if (g_pCodeWindow->m_WatchWindow)
+					g_pCodeWindow->m_WatchWindow->LoadAll();
+				if (g_pCodeWindow->m_BreakpointWindow)
+					g_pCodeWindow->m_BreakpointWindow->LoadAll();
+			}
+		}
+	}
 }
 
 // Open file to boot
@@ -1163,6 +1177,25 @@ void CFrame::DoStop()
 			}
 		}
 
+		if (UseDebugger)
+		{
+			if (g_pCodeWindow)
+			{
+				if (g_pCodeWindow->m_WatchWindow)
+				{
+					g_pCodeWindow->m_WatchWindow->SaveAll();
+					PowerPC::watches.Clear();
+				}
+				if (g_pCodeWindow->m_BreakpointWindow)
+				{
+					g_pCodeWindow->m_BreakpointWindow->SaveAll();
+					PowerPC::breakpoints.Clear();
+					PowerPC::memchecks.Clear();
+					g_pCodeWindow->m_BreakpointWindow->NotifyUpdate();
+				}
+			}
+		}
+
 		// TODO: Show the author/description dialog here
 		if (Movie::IsRecordingInput())
 			DoRecordingSave();