diff --git a/Source/Core/Core/ActionReplay.cpp b/Source/Core/Core/ActionReplay.cpp
index 24e54259e3..f3641f72bc 100644
--- a/Source/Core/Core/ActionReplay.cpp
+++ b/Source/Core/Core/ActionReplay.cpp
@@ -266,6 +266,12 @@ std::vector<ARCode> LoadCodes(const IniFile& global_ini, const IniFile& local_in
     }
 
     ReadEnabledAndDisabled(*ini, "ActionReplay", &codes);
+
+    if (ini == &global_ini)
+    {
+      for (ARCode& code : codes)
+        code.default_enabled = code.enabled;
+    }
   }
 
   return codes;
@@ -275,21 +281,27 @@ void SaveCodes(IniFile* local_ini, const std::vector<ARCode>& codes)
 {
   std::vector<std::string> lines;
   std::vector<std::string> enabled_lines;
+  std::vector<std::string> disabled_lines;
+
   for (const ActionReplay::ARCode& code : codes)
   {
     if (code.enabled)
-      enabled_lines.emplace_back("$" + code.name);
+      enabled_lines.emplace_back('$' + code.name);
+    else if (code.default_enabled)
+      disabled_lines.emplace_back('$' + code.name);
 
     if (code.user_defined)
     {
-      lines.emplace_back("$" + code.name);
+      lines.emplace_back('$' + code.name);
       for (const ActionReplay::AREntry& op : code.ops)
       {
         lines.emplace_back(fmt::format("{:08X} {:08X}", op.cmd_addr, op.value));
       }
     }
   }
+
   local_ini->SetLines("ActionReplay_Enabled", enabled_lines);
+  local_ini->SetLines("ActionReplay_Disabled", disabled_lines);
   local_ini->SetLines("ActionReplay", lines);
 }
 
diff --git a/Source/Core/Core/ActionReplay.h b/Source/Core/Core/ActionReplay.h
index bd93503f52..e79c6d4f38 100644
--- a/Source/Core/Core/ActionReplay.h
+++ b/Source/Core/Core/ActionReplay.h
@@ -29,6 +29,7 @@ struct ARCode
   std::string name;
   std::vector<AREntry> ops;
   bool enabled = false;
+  bool default_enabled = false;
   bool user_defined = false;
 };
 
diff --git a/Source/Core/Core/GeckoCode.h b/Source/Core/Core/GeckoCode.h
index 9c6c7c7a14..74d750bcf4 100644
--- a/Source/Core/Core/GeckoCode.h
+++ b/Source/Core/Core/GeckoCode.h
@@ -29,6 +29,7 @@ public:
   std::vector<std::string> notes;
 
   bool enabled = false;
+  bool default_enabled = false;
   bool user_defined = false;
 
   bool Exist(u32 address, u32 data) const;
diff --git a/Source/Core/Core/GeckoCodeConfig.cpp b/Source/Core/Core/GeckoCodeConfig.cpp
index 32ea337af3..605fb82533 100644
--- a/Source/Core/Core/GeckoCodeConfig.cpp
+++ b/Source/Core/Core/GeckoCodeConfig.cpp
@@ -192,6 +192,12 @@ std::vector<GeckoCode> LoadCodes(const IniFile& globalIni, const IniFile& localI
     }
 
     ReadEnabledAndDisabled(*ini, "Gecko", &gcodes);
+
+    if (ini == &globalIni)
+    {
+      for (GeckoCode& code : gcodes)
+        code.default_enabled = code.enabled;
+    }
   }
 
   return gcodes;
@@ -210,12 +216,8 @@ static std::string MakeGeckoCodeTitle(const GeckoCode& code)
 }
 
 // used by the SaveGeckoCodes function
-static void SaveGeckoCode(std::vector<std::string>& lines, std::vector<std::string>& enabledLines,
-                          const GeckoCode& gcode)
+static void SaveGeckoCode(std::vector<std::string>& lines, const GeckoCode& gcode)
 {
-  if (gcode.enabled)
-    enabledLines.push_back('$' + gcode.name);
-
   if (!gcode.user_defined)
     return;
 
@@ -235,14 +237,21 @@ static void SaveGeckoCode(std::vector<std::string>& lines, std::vector<std::stri
 void SaveCodes(IniFile& inifile, const std::vector<GeckoCode>& gcodes)
 {
   std::vector<std::string> lines;
-  std::vector<std::string> enabledLines;
+  std::vector<std::string> enabled_lines;
+  std::vector<std::string> disabled_lines;
 
   for (const GeckoCode& geckoCode : gcodes)
   {
-    SaveGeckoCode(lines, enabledLines, geckoCode);
+    if (geckoCode.enabled)
+      enabled_lines.emplace_back('$' + geckoCode.name);
+    else if (geckoCode.default_enabled)
+      disabled_lines.emplace_back('$' + geckoCode.name);
+
+    SaveGeckoCode(lines, geckoCode);
   }
 
   inifile.SetLines("Gecko", lines);
-  inifile.SetLines("Gecko_Enabled", enabledLines);
+  inifile.SetLines("Gecko_Enabled", enabled_lines);
+  inifile.SetLines("Gecko_Disabled", disabled_lines);
 }
 }  // namespace Gecko
diff --git a/Source/Core/Core/PatchEngine.cpp b/Source/Core/Core/PatchEngine.cpp
index 3e395fdc6c..4f4daafcd7 100644
--- a/Source/Core/Core/PatchEngine.cpp
+++ b/Source/Core/Core/PatchEngine.cpp
@@ -110,6 +110,12 @@ void LoadPatchSection(const std::string& section, std::vector<Patch>& patches, I
     }
 
     ReadEnabledAndDisabled(*ini, section, &patches);
+
+    if (ini == &globalIni)
+    {
+      for (Patch& patch : patches)
+        patch.default_enabled = patch.enabled;
+    }
   }
 }
 
diff --git a/Source/Core/Core/PatchEngine.h b/Source/Core/Core/PatchEngine.h
index 97386b6a9a..a496f04936 100644
--- a/Source/Core/Core/PatchEngine.h
+++ b/Source/Core/Core/PatchEngine.h
@@ -34,6 +34,7 @@ struct Patch
   std::string name;
   std::vector<PatchEntry> entries;
   bool enabled = false;
+  bool default_enabled = false;
   bool user_defined = false;  // False if this code is shipped with Dolphin.
 };
 
diff --git a/Source/Core/DolphinQt/Config/PatchesWidget.cpp b/Source/Core/DolphinQt/Config/PatchesWidget.cpp
index 724780e199..1ac7f55154 100644
--- a/Source/Core/DolphinQt/Config/PatchesWidget.cpp
+++ b/Source/Core/DolphinQt/Config/PatchesWidget.cpp
@@ -129,21 +129,24 @@ void PatchesWidget::SavePatches()
 {
   std::vector<std::string> lines;
   std::vector<std::string> lines_enabled;
+  std::vector<std::string> lines_disabled;
 
   for (const auto& patch : m_patches)
   {
     if (patch.enabled)
-      lines_enabled.push_back("$" + patch.name);
+      lines_enabled.emplace_back('$' + patch.name);
+    else if (patch.default_enabled)
+      lines_disabled.emplace_back('$' + patch.name);
 
     if (!patch.user_defined)
       continue;
 
-    lines.push_back("$" + patch.name);
+    lines.emplace_back('$' + patch.name);
 
     for (const auto& entry : patch.entries)
     {
-      lines.push_back(StringFromFormat("0x%08X:%s:0x%08X", entry.address,
-                                       PatchEngine::PatchTypeAsString(entry.type), entry.value));
+      lines.emplace_back(StringFromFormat("0x%08X:%s:0x%08X", entry.address,
+                                          PatchEngine::PatchTypeAsString(entry.type), entry.value));
     }
   }
 
@@ -151,6 +154,7 @@ void PatchesWidget::SavePatches()
   game_ini_local.Load(File::GetUserPath(D_GAMESETTINGS_IDX) + m_game_id + ".ini");
 
   game_ini_local.SetLines("OnFrame_Enabled", lines_enabled);
+  game_ini_local.SetLines("OnFrame_Disabled", lines_disabled);
   game_ini_local.SetLines("OnFrame", lines);
 
   game_ini_local.Save(File::GetUserPath(D_GAMESETTINGS_IDX) + m_game_id + ".ini");