diff --git a/Source/Core/Core/PatchEngine.cpp b/Source/Core/Core/PatchEngine.cpp
@@ -12,7 +12,6 @@
 #include <array>
 #include <iterator>
 #include <map>
-#include <set>
 #include <string>
 #include <vector>
 
@@ -21,6 +20,7 @@
 #include "Common/StringUtil.h"
 
 #include "Core/ActionReplay.h"
+#include "Core/CheatCodes.h"
 #include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
 #include "Core/GeckoCode.h"
@@ -47,20 +47,6 @@ const char* PatchTypeAsString(PatchType type)
 void LoadPatchSection(const std::string& section, std::vector<Patch>& patches, IniFile& globalIni,
                       IniFile& localIni)
 {
-  // Load the name of all enabled patches
-  std::string enabledSectionName = section + "_Enabled";
-  std::vector<std::string> enabledLines;
-  std::set<std::string> enabledNames;
-  localIni.GetLines(enabledSectionName, &enabledLines);
-  for (const std::string& line : enabledLines)
-  {
-    if (!line.empty() && line[0] == '$')
-    {
-      std::string name = line.substr(1, line.size() - 1);
-      enabledNames.insert(name);
-    }
-  }
-
   const IniFile* inis[2] = {&globalIni, &localIni};
 
   for (const IniFile* ini : inis)
@@ -83,9 +69,8 @@ void LoadPatchSection(const std::string& section, std::vector<Patch>& patches, I
         }
         currentPatch.entries.clear();
 
-        // Set active and name
+        // Set name and whether the patch is user defined
         currentPatch.name = line.substr(1, line.size() - 1);
-        currentPatch.active = enabledNames.find(currentPatch.name) != enabledNames.end();
         currentPatch.user_defined = (ini == &localIni);
       }
       else
@@ -123,6 +108,14 @@ void LoadPatchSection(const std::string& section, std::vector<Patch>& patches, I
     {
       patches.push_back(currentPatch);
     }
+
+    ReadEnabledAndDisabled(*ini, section, &patches);
+
+    if (ini == &globalIni)
+    {
+      for (Patch& patch : patches)
+        patch.default_enabled = patch.enabled;
+    }
   }
 }
 
@@ -185,7 +178,7 @@ static void ApplyPatches(const std::vector<Patch>& patches)
 {
   for (const Patch& patch : patches)
   {
-    if (patch.active)
+    if (patch.enabled)
     {
       for (const PatchEntry& entry : patch.entries)
       {

diff --git a/Source/Core/Core/PatchEngine.h b/Source/Core/Core/PatchEngine.h
@@ -33,7 +33,8 @@ struct Patch
 {
   std::string name;
   std::vector<PatchEntry> entries;
-  bool active = false;
+  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/CheatsManager.cpp b/Source/Core/DolphinQt/CheatsManager.cpp
@@ -292,7 +292,7 @@ void CheatsManager::GenerateARCode()
   int index = item->data(INDEX_ROLE).toInt();
   ActionReplay::ARCode ar_code;
 
-  ar_code.active = true;
+  ar_code.enabled = true;
   ar_code.user_defined = true;
   ar_code.name = tr("Generated by search (Address %1)")
                      .arg(m_watch[index].address, 8, 16, QLatin1Char('0'))

diff --git a/Source/Core/DolphinQt/Config/ARCodeWidget.cpp b/Source/Core/DolphinQt/Config/ARCodeWidget.cpp
@@ -89,7 +89,7 @@ void ARCodeWidget::ConnectWidgets()
 
 void ARCodeWidget::OnItemChanged(QListWidgetItem* item)
 {
-  m_ar_codes[m_code_list->row(item)].active = (item->checkState() == Qt::Checked);
+  m_ar_codes[m_code_list->row(item)].enabled = (item->checkState() == Qt::Checked);
 
   if (!m_restart_required)
     ActionReplay::ApplyCodes(m_ar_codes);
@@ -159,7 +159,7 @@ void ARCodeWidget::UpdateList()
 
     item->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable | Qt::ItemIsUserCheckable |
                    Qt::ItemIsDragEnabled);
-    item->setCheckState(ar.active ? Qt::Checked : Qt::Unchecked);
+    item->setCheckState(ar.enabled ? Qt::Checked : Qt::Unchecked);
     item->setData(Qt::UserRole, static_cast<int>(i));
 
     m_code_list->addItem(item);
@@ -190,7 +190,7 @@ void ARCodeWidget::AddCode(ActionReplay::ARCode code)
 void ARCodeWidget::OnCodeAddClicked()
 {
   ActionReplay::ARCode ar;
-  ar.active = true;
+  ar.enabled = true;
 
   CheatCodeEditor ed(this);
   ed.SetARCode(&ar);

diff --git a/Source/Core/DolphinQt/Config/NewPatchDialog.cpp b/Source/Core/DolphinQt/Config/NewPatchDialog.cpp
@@ -34,7 +34,7 @@ NewPatchDialog::NewPatchDialog(QWidget* parent, PatchEngine::Patch& patch)
   if (m_patch.entries.empty())
   {
     AddEntry();
-    m_patch.active = true;
+    m_patch.enabled = true;
   }
 }
 

diff --git a/Source/Core/DolphinQt/Config/PatchesWidget.cpp b/Source/Core/DolphinQt/Config/PatchesWidget.cpp
@@ -65,7 +65,7 @@ void PatchesWidget::ConnectWidgets()
 
 void PatchesWidget::OnItemChanged(QListWidgetItem* item)
 {
-  m_patches[m_list->row(item)].active = (item->checkState() == Qt::Checked);
+  m_patches[m_list->row(item)].enabled = (item->checkState() == Qt::Checked);
   SavePatches();
 }
 
@@ -129,28 +129,32 @@ 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.active)
-      lines_enabled.push_back("$" + patch.name);
+    if (patch.enabled)
+      lines_enabled.emplace_back('$' + 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));
     }
   }
 
   IniFile game_ini_local;
   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");
@@ -164,7 +168,7 @@ void PatchesWidget::Update()
   {
     auto* item = new QListWidgetItem(QString::fromStdString(patch.name));
     item->setFlags(item->flags() | Qt::ItemIsUserCheckable);
-    item->setCheckState(patch.active ? Qt::Checked : Qt::Unchecked);
+    item->setCheckState(patch.enabled ? Qt::Checked : Qt::Unchecked);
     item->setData(Qt::UserRole, patch.user_defined);
 
     m_list->addItem(item);