diff --git a/Source/Core/Core/CMakeLists.txt b/Source/Core/Core/CMakeLists.txt
index 5caf9dc882..e5ba06faac 100644
--- a/Source/Core/Core/CMakeLists.txt
+++ b/Source/Core/Core/CMakeLists.txt
@@ -28,6 +28,7 @@ set(SRCS
   Config/Config.cpp
   ConfigLoaders/BaseConfigLoader.cpp
   ConfigLoaders/GameConfigLoader.cpp
+  ConfigLoaders/IsSettingSaveable.cpp
   ConfigLoaders/MovieConfigLoader.cpp
   ConfigLoaders/NetPlayConfigLoader.cpp
   Debugger/Debugger_SymbolMap.cpp
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index 42f66de233..25cb3f358b 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -16,6 +16,7 @@
 
 #include "Core/Config/Config.h"
 #include "Core/ConfigLoaders/BaseConfigLoader.h"
+#include "Core/ConfigLoaders/IsSettingSaveable.h"
 
 namespace ConfigLoaders
 {
@@ -80,7 +81,12 @@ public:
         IniFile::Section* ini_section = ini.GetOrCreateSection(section_name);
 
         for (const auto& value : section_values)
+        {
+          if (!IsSettingSaveable({system.first, section->GetName(), value.first}))
+            continue;
+
           ini_section->Set(value.first, value.second);
+        }
       }
 
       ini.Save(File::GetUserPath(mapping->second));
diff --git a/Source/Core/Core/ConfigLoaders/GameConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/GameConfigLoader.cpp
index 56aa711b59..05544c303a 100644
--- a/Source/Core/Core/ConfigLoaders/GameConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/GameConfigLoader.cpp
@@ -20,6 +20,7 @@
 
 #include "Core/Config/Config.h"
 #include "Core/ConfigLoaders/GameConfigLoader.h"
+#include "Core/ConfigLoaders/IsSettingSaveable.h"
 
 namespace ConfigLoaders
 {
@@ -382,6 +383,9 @@ void INIGameConfigLayerLoader::Save(Config::Layer* config_layer)
     {
       for (const auto& value : section->GetValues())
       {
+        if (!IsSettingSaveable({system.first, section->GetName(), value.first}))
+          continue;
+
         const auto ini_location =
             GetINILocationFromConfig({system.first, section->GetName(), value.first});
         if (ini_location.first.empty() && ini_location.second.empty())
diff --git a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
new file mode 100644
index 0000000000..1cd3da88d2
--- /dev/null
+++ b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
@@ -0,0 +1,20 @@
+// Copyright 2017 Dolphin Emulator Project
+// Licensed under GPLv2+
+// Refer to the license.txt file included.
+
+#include <algorithm>
+#include <vector>
+
+#include "Core/Config/Config.h"
+#include "Core/ConfigLoaders/IsSettingSaveable.h"
+
+namespace ConfigLoaders
+{
+const static std::vector<Config::ConfigLocation> s_setting_saveable{};
+
+bool IsSettingSaveable(const Config::ConfigLocation& config_location)
+{
+  return std::find(s_setting_saveable.begin(), s_setting_saveable.end(), config_location) !=
+         s_setting_saveable.end();
+}
+}  // namespace ConfigLoader
diff --git a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.h b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.h
new file mode 100644
index 0000000000..86a7939c5d
--- /dev/null
+++ b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.h
@@ -0,0 +1,18 @@
+// Copyright 2017 Dolphin Emulator Project
+// Licensed under GPLv2+
+// Refer to the license.txt file included.
+
+#pragma once
+
+namespace Config
+{
+struct ConfigLocation;
+}
+
+namespace ConfigLoaders
+{
+// This is a temporary function that allows for both the new and old configuration
+// systems to co-exist without trampling on each other while saving.
+// This function shall be removed when the old configuration system retires.
+bool IsSettingSaveable(const Config::ConfigLocation& config_location);
+}  // namespace ConfigLoader
diff --git a/Source/Core/Core/Core.vcxproj b/Source/Core/Core/Core.vcxproj
index 615d2c7857..d1c648a78d 100644
--- a/Source/Core/Core/Core.vcxproj
+++ b/Source/Core/Core/Core.vcxproj
@@ -59,6 +59,7 @@
     <ClCompile Include="Config\Config.cpp" />
     <ClCompile Include="ConfigLoaders\BaseConfigLoader.cpp" />
     <ClCompile Include="ConfigLoaders\GameConfigLoader.cpp" />
+    <ClCompile Include="ConfigLoaders\IsSettingSaveable.cpp" />
     <ClCompile Include="ConfigLoaders\MovieConfigLoader.cpp" />
     <ClCompile Include="ConfigLoaders\NetPlayConfigLoader.cpp" />
     <ClCompile Include="ConfigManager.cpp" />
@@ -311,6 +312,7 @@
     <ClInclude Include="Config\Config.h" />
     <ClInclude Include="ConfigLoaders\BaseConfigLoader.h" />
     <ClInclude Include="ConfigLoaders\GameConfigLoader.h" />
+    <ClInclude Include="ConfigLoaders\IsSettingSaveable.h" />
     <ClInclude Include="ConfigLoaders\MovieConfigLoader.h" />
     <ClInclude Include="ConfigLoaders\NetPlayConfigLoader.h" />
     <ClInclude Include="ConfigManager.h" />
diff --git a/Source/Core/Core/Core.vcxproj.filters b/Source/Core/Core/Core.vcxproj.filters
index f390cd99b3..8f9a620aa8 100644
--- a/Source/Core/Core/Core.vcxproj.filters
+++ b/Source/Core/Core/Core.vcxproj.filters
@@ -853,6 +853,9 @@
     <ClCompile Include="ConfigLoaders\NetPlayConfigLoader.cpp">
       <Filter>ConfigLoader</Filter>
     </ClCompile>
+    <ClCompile Include="ConfigLoaders\IsSettingSaveable.cpp">
+      <Filter>ConfigLoader</Filter>
+    </ClCompile>
     <ClCompile Include="Config\Config.cpp" />
   </ItemGroup>
   <ItemGroup>
@@ -1488,6 +1491,9 @@
       <Filter>ConfigLoader</Filter>
     </ClInclude>
     <ClInclude Include="Config\Config.h" />
+    <ClInclude Include="ConfigLoaders\IsSettingSaveable.h">
+      <Filter>ConfigLoader</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <Text Include="CMakeLists.txt" />