diff --git a/Source/Core/Common/CMakeLists.txt b/Source/Core/Common/CMakeLists.txt
index 15c79c3d3b..6ef614a325 100644
--- a/Source/Core/Common/CMakeLists.txt
+++ b/Source/Core/Common/CMakeLists.txt
@@ -34,7 +34,6 @@ add_library(common
   SettingsHandler.cpp
   StringUtil.cpp
   SymbolDB.cpp
-  SysConf.cpp
   Thread.cpp
   Timer.cpp
   TraversalClient.cpp
diff --git a/Source/Core/Common/Common.vcxproj b/Source/Core/Common/Common.vcxproj
index 5b64898b7b..05a86d667c 100644
--- a/Source/Core/Common/Common.vcxproj
+++ b/Source/Core/Common/Common.vcxproj
@@ -147,7 +147,6 @@
     <ClInclude Include="StringUtil.h" />
     <ClInclude Include="Swap.h" />
     <ClInclude Include="SymbolDB.h" />
-    <ClInclude Include="SysConf.h" />
     <ClInclude Include="Thread.h" />
     <ClInclude Include="Timer.h" />
     <ClInclude Include="TraversalClient.h" />
@@ -203,7 +202,6 @@
     <ClCompile Include="SettingsHandler.cpp" />
     <ClCompile Include="StringUtil.cpp" />
     <ClCompile Include="SymbolDB.cpp" />
-    <ClCompile Include="SysConf.cpp" />
     <ClCompile Include="Thread.cpp" />
     <ClCompile Include="Timer.cpp" />
     <ClCompile Include="TraversalClient.cpp" />
diff --git a/Source/Core/Common/Common.vcxproj.filters b/Source/Core/Common/Common.vcxproj.filters
index 58b75ff30f..8dd8bd6aeb 100644
--- a/Source/Core/Common/Common.vcxproj.filters
+++ b/Source/Core/Common/Common.vcxproj.filters
@@ -67,7 +67,6 @@
     <ClInclude Include="StringUtil.h" />
     <ClInclude Include="Swap.h" />
     <ClInclude Include="SymbolDB.h" />
-    <ClInclude Include="SysConf.h" />
     <ClInclude Include="Thread.h" />
     <ClInclude Include="Timer.h" />
     <ClInclude Include="Version.h" />
@@ -289,7 +288,6 @@
     <ClCompile Include="SettingsHandler.cpp" />
     <ClCompile Include="StringUtil.cpp" />
     <ClCompile Include="SymbolDB.cpp" />
-    <ClCompile Include="SysConf.cpp" />
     <ClCompile Include="Thread.cpp" />
     <ClCompile Include="Timer.cpp" />
     <ClCompile Include="Version.cpp" />
diff --git a/Source/Core/Core/CMakeLists.txt b/Source/Core/Core/CMakeLists.txt
index 58a5254cb8..26ab98f803 100644
--- a/Source/Core/Core/CMakeLists.txt
+++ b/Source/Core/Core/CMakeLists.txt
@@ -16,6 +16,7 @@ add_library(core
   NetPlayServer.cpp
   PatchEngine.cpp
   State.cpp
+  SysConf.cpp
   TitleDatabase.cpp
   WiiRoot.cpp
   WiiUtils.cpp
diff --git a/Source/Core/Core/Config/SYSCONFSettings.h b/Source/Core/Core/Config/SYSCONFSettings.h
index f4ade3ddf8..2d1dd78e12 100644
--- a/Source/Core/Core/Config/SYSCONFSettings.h
+++ b/Source/Core/Core/Config/SYSCONFSettings.h
@@ -8,7 +8,7 @@
 #include <variant>
 
 #include "Common/Config/Config.h"
-#include "Common/SysConf.h"
+#include "Core/SysConf.h"
 
 namespace Config
 {
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index 4dcfb613ae..8d6e00fe20 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -17,12 +17,13 @@
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
 #include "Common/Logging/Log.h"
-#include "Common/SysConf.h"
 
 #include "Core/Config/SYSCONFSettings.h"
 #include "Core/ConfigLoaders/IsSettingSaveable.h"
 #include "Core/Core.h"
+#include "Core/IOS/IOS.h"
 #include "Core/IOS/USB/Bluetooth/BTBase.h"
+#include "Core/SysConf.h"
 
 namespace ConfigLoaders
 {
@@ -31,7 +32,8 @@ void SaveToSYSCONF(Config::LayerType layer)
   if (Core::IsRunning())
     return;
 
-  SysConf sysconf{Common::FromWhichRoot::FROM_CONFIGURED_ROOT};
+  IOS::HLE::Kernel ios;
+  SysConf sysconf{ios.GetFS()};
 
   for (const Config::SYSCONFSetting& setting : Config::SYSCONF_SETTINGS)
   {
@@ -154,7 +156,8 @@ private:
     if (Core::IsRunning())
       return;
 
-    SysConf sysconf{Common::FromWhichRoot::FROM_CONFIGURED_ROOT};
+    IOS::HLE::Kernel ios;
+    SysConf sysconf{ios.GetFS()};
     for (const Config::SYSCONFSetting& setting : Config::SYSCONF_SETTINGS)
     {
       std::visit(
diff --git a/Source/Core/Core/Core.vcxproj b/Source/Core/Core/Core.vcxproj
index 641aaeaaab..3a1aeee2ea 100644
--- a/Source/Core/Core/Core.vcxproj
+++ b/Source/Core/Core/Core.vcxproj
@@ -292,6 +292,7 @@
     <ClCompile Include="PowerPC\PPCTables.cpp" />
     <ClCompile Include="PowerPC\Profiler.cpp" />
     <ClCompile Include="State.cpp" />
+    <ClCompile Include="SysConf.cpp" />
     <ClCompile Include="TitleDatabase.cpp" />
     <ClCompile Include="WiiRoot.cpp" />
     <ClCompile Include="WiiUtils.cpp" />
@@ -530,6 +531,7 @@
     <ClInclude Include="PowerPC\PPCTables.h" />
     <ClInclude Include="PowerPC\Profiler.h" />
     <ClInclude Include="State.h" />
+    <ClInclude Include="SysConf.h" />
     <ClInclude Include="Titles.h" />
     <ClInclude Include="TitleDatabase.h" />
     <ClInclude Include="WiiRoot.h" />
diff --git a/Source/Core/Core/Core.vcxproj.filters b/Source/Core/Core/Core.vcxproj.filters
index 5456cd4be5..25a151d371 100644
--- a/Source/Core/Core/Core.vcxproj.filters
+++ b/Source/Core/Core/Core.vcxproj.filters
@@ -179,6 +179,7 @@
     <ClCompile Include="NetPlayServer.cpp" />
     <ClCompile Include="PatchEngine.cpp" />
     <ClCompile Include="State.cpp" />
+    <ClCompile Include="SysConf.cpp" />
     <ClCompile Include="TitleDatabase.cpp" />
     <ClCompile Include="WiiRoot.cpp" />
     <ClCompile Include="WiiUtils.cpp" />
@@ -912,6 +913,7 @@
     <ClInclude Include="NetPlayServer.h" />
     <ClInclude Include="PatchEngine.h" />
     <ClInclude Include="State.h" />
+    <ClInclude Include="SysConf.h" />
     <ClInclude Include="Titles.h" />
     <ClInclude Include="TitleDatabase.h" />
     <ClInclude Include="WiiRoot.h" />
diff --git a/Source/Core/Core/IOS/FS/FileSystem.cpp b/Source/Core/Core/IOS/FS/FileSystem.cpp
index 552d68ec8b..f2beb7d0c8 100644
--- a/Source/Core/Core/IOS/FS/FileSystem.cpp
+++ b/Source/Core/Core/IOS/FS/FileSystem.cpp
@@ -28,7 +28,7 @@ FileHandle::FileHandle(FileHandle&& other) : m_fs{other.m_fs}, m_fd{other.m_fd}
 
 FileHandle& FileHandle::operator=(FileHandle&& other)
 {
-  if (*this != other)
+  if (std::tie(m_fs, m_fd) != std::tie(other.m_fs, other.m_fd))
     *this = std::move(other);
   return *this;
 }
@@ -46,6 +46,16 @@ Fd FileHandle::Release()
   return fd;
 }
 
+Result<u32> FileHandle::Seek(u32 offset, SeekMode mode) const
+{
+  return m_fs->SeekFile(*m_fd, offset, mode);
+}
+
+Result<FileStatus> FileHandle::GetStatus() const
+{
+  return m_fs->GetFileStatus(*m_fd);
+}
+
 void FileSystem::Init()
 {
   if (Delete(0, 0, "/tmp") == ResultCode::Success)
diff --git a/Source/Core/Core/IOS/FS/FileSystem.h b/Source/Core/Core/IOS/FS/FileSystem.h
index 87890cdbad..eb14dc6673 100644
--- a/Source/Core/Core/IOS/FS/FileSystem.h
+++ b/Source/Core/Core/IOS/FS/FileSystem.h
@@ -108,10 +108,18 @@ public:
   FileHandle& operator=(const FileHandle&) = delete;
   FileHandle& operator=(FileHandle&&);
 
-  operator Fd() const { return m_fd.value(); }
   /// Release the FD so that it is not automatically closed.
   Fd Release();
 
+  template <typename T>
+  Result<size_t> Read(T* ptr, size_t count) const;
+
+  template <typename T>
+  Result<size_t> Write(const T* ptr, size_t count) const;
+
+  Result<u32> Seek(u32 offset, SeekMode mode) const;
+  Result<FileStatus> GetStatus() const;
+
 private:
   FileSystem* m_fs;
   std::optional<Fd> m_fd;
@@ -140,26 +148,6 @@ public:
   /// Get status for a file descriptor.
   virtual Result<FileStatus> GetFileStatus(Fd fd) = 0;
 
-  template <typename T>
-  Result<u32> ReadFile(Fd fd, T* ptr, u32 count)
-  {
-    const Result<u32> bytes = ReadBytesFromFile(fd, reinterpret_cast<u8*>(ptr), sizeof(T) * count);
-    if (!bytes)
-      return bytes.Error();
-    if (*bytes != sizeof(T) * count)
-      return ResultCode::ShortRead;
-    return count;
-  }
-
-  template <typename T>
-  Result<u32> WriteFile(Fd fd, const T* ptr, u32 count)
-  {
-    const auto result = WriteBytesToFile(fd, reinterpret_cast<const u8*>(ptr), sizeof(T) * count);
-    if (!result)
-      return result.Error();
-    return count;
-  }
-
   /// Create a file with the specified path and metadata.
   virtual ResultCode CreateFile(Uid caller_uid, Gid caller_gid, const std::string& path,
                                 FileAttribute attribute, Mode owner_mode, Mode group_mode,
@@ -195,6 +183,28 @@ protected:
   void Init();
 };
 
+template <typename T>
+Result<size_t> FileHandle::Read(T* ptr, size_t count) const
+{
+  const Result<u32> bytes = m_fs->ReadBytesFromFile(*m_fd, reinterpret_cast<u8*>(ptr),
+                                                    static_cast<u32>(sizeof(T) * count));
+  if (!bytes)
+    return bytes.Error();
+  if (*bytes != sizeof(T) * count)
+    return ResultCode::ShortRead;
+  return count;
+}
+
+template <typename T>
+Result<size_t> FileHandle::Write(const T* ptr, size_t count) const
+{
+  const auto result = m_fs->WriteBytesToFile(*m_fd, reinterpret_cast<const u8*>(ptr),
+                                             static_cast<u32>(sizeof(T) * count));
+  if (!result)
+    return result.Error();
+  return count;
+}
+
 enum class Location
 {
   Configured,
diff --git a/Source/Core/Core/IOS/USB/Bluetooth/BTBase.cpp b/Source/Core/Core/IOS/USB/Bluetooth/BTBase.cpp
index c4770253d6..b1fadd8a1f 100644
--- a/Source/Core/Core/IOS/USB/Bluetooth/BTBase.cpp
+++ b/Source/Core/Core/IOS/USB/Bluetooth/BTBase.cpp
@@ -13,7 +13,7 @@
 #include "Common/File.h"
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
-#include "Common/SysConf.h"
+#include "Core/SysConf.h"
 
 namespace IOS
 {
diff --git a/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp b/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp
index 11b0da139e..454eddc37b 100644
--- a/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp
+++ b/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp
@@ -15,7 +15,6 @@
 #include "Common/MsgHandler.h"
 #include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
-#include "Common/SysConf.h"
 #include "Core/Core.h"
 #include "Core/CoreTiming.h"
 #include "Core/Debugger/Debugger_SymbolMap.h"
@@ -25,6 +24,7 @@
 #include "Core/Host.h"
 #include "Core/IOS/Device.h"
 #include "Core/IOS/IOS.h"
+#include "Core/SysConf.h"
 #include "InputCommon/ControllerInterface/ControllerInterface.h"
 
 namespace IOS
@@ -42,8 +42,7 @@ namespace Device
 BluetoothEmu::BluetoothEmu(Kernel& ios, const std::string& device_name)
     : BluetoothBase(ios, device_name)
 {
-  SysConf sysconf{Core::WantsDeterminism() ? Common::FromWhichRoot::FROM_SESSION_ROOT :
-                                             Common::FromWhichRoot::FROM_CONFIGURED_ROOT};
+  SysConf sysconf{ios.GetFS()};
   if (!Core::WantsDeterminism())
     BackUpBTInfoSection(&sysconf);
 
diff --git a/Source/Core/Common/SysConf.cpp b/Source/Core/Core/SysConf.cpp
similarity index 85%
rename from Source/Core/Common/SysConf.cpp
rename to Source/Core/Core/SysConf.cpp
index 22e902d042..6efb18a729 100644
--- a/Source/Core/Common/SysConf.cpp
+++ b/Source/Core/Core/SysConf.cpp
@@ -2,7 +2,7 @@
 // Licensed under GPLv2+
 // Refer to the license.txt file included.
 
-#include "Common/SysConf.h"
+#include "Core/SysConf.h"
 
 #include <algorithm>
 #include <array>
@@ -14,6 +14,7 @@
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
 #include "Common/Swap.h"
+#include "Core/IOS/FS/FileSystem.h"
 
 constexpr size_t SYSCONF_SIZE = 0x4000;
 
@@ -35,9 +36,8 @@ static size_t GetNonArrayEntrySize(SysConf::Entry::Type type)
     return 0;
   }
 }
-SysConf::SysConf(const Common::FromWhichRoot root_type)
+SysConf::SysConf(std::shared_ptr<IOS::HLE::FS::FileSystem> fs) : m_fs{fs}
 {
-  m_file_name = Common::RootUserPath(root_type) + DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF;
   Load();
 }
 
@@ -55,39 +55,40 @@ void SysConf::Load()
 {
   Clear();
 
-  if (File::GetSize(m_file_name) != SYSCONF_SIZE || !LoadFromFile(m_file_name))
+  const auto file = m_fs->OpenFile(IOS::HLE::FS::Uid{0}, IOS::HLE::FS::Gid{0},
+                                   "/shared2/sys/SYSCONF", IOS::HLE::FS::Mode::Read);
+  if (!file || file->GetStatus()->size != SYSCONF_SIZE || !LoadFromFile(*file))
   {
     WARN_LOG(CORE, "No valid SYSCONF detected. Creating a new one.");
     InsertDefaultEntries();
   }
 }
 
-bool SysConf::LoadFromFile(const std::string& file_name)
+bool SysConf::LoadFromFile(const IOS::HLE::FS::FileHandle& file)
 {
-  File::IOFile file(file_name, "rb");
-  file.Seek(4, SEEK_SET);
+  file.Seek(4, IOS::HLE::FS::SeekMode::Set);
   u16 number_of_entries;
-  file.ReadBytes(&number_of_entries, sizeof(number_of_entries));
+  file.Read(&number_of_entries, 1);
   number_of_entries = Common::swap16(number_of_entries);
 
   std::vector<u16> offsets(number_of_entries);
   for (u16& offset : offsets)
   {
-    file.ReadBytes(&offset, sizeof(offset));
+    file.Read(&offset, 1);
     offset = Common::swap16(offset);
   }
 
   for (const u16 offset : offsets)
   {
-    file.Seek(offset, SEEK_SET);
+    file.Seek(offset, IOS::HLE::FS::SeekMode::Set);
 
     // Metadata
     u8 description = 0;
-    file.ReadBytes(&description, sizeof(description));
+    file.Read(&description, 1);
     const Entry::Type type = static_cast<Entry::Type>((description & 0xe0) >> 5);
     const u8 name_length = (description & 0x1f) + 1;
     std::string name(name_length, '\0');
-    file.ReadBytes(&name[0], name.size());
+    file.Read(&name[0], name.size());
 
     // Data
     std::vector<u8> data;
@@ -96,7 +97,7 @@ bool SysConf::LoadFromFile(const std::string& file_name)
     case Entry::Type::BigArray:
     {
       u16 data_length = 0;
-      file.ReadBytes(&data_length, sizeof(data_length));
+      file.Read(&data_length, 1);
       // The stored u16 is length - 1, not length.
       data.resize(Common::swap16(data_length) + 1);
       break;
@@ -104,7 +105,7 @@ bool SysConf::LoadFromFile(const std::string& file_name)
     case Entry::Type::SmallArray:
     {
       u8 data_length = 0;
-      file.ReadBytes(&data_length, sizeof(data_length));
+      file.Read(&data_length, 1);
       data.resize(data_length + 1);
       break;
     }
@@ -121,7 +122,7 @@ bool SysConf::LoadFromFile(const std::string& file_name)
       return false;
     }
 
-    file.ReadBytes(data.data(), data.size());
+    file.Read(data.data(), data.size());
     AddEntry({type, name, std::move(data)});
   }
   return true;
@@ -194,14 +195,19 @@ bool SysConf::Save() const
   std::copy(footer.cbegin(), footer.cend(), buffer.end() - footer.size());
 
   // Write the new data.
-  const std::string temp_file = m_file_name + ".tmp";
-  File::CreateFullPath(temp_file);
+  const std::string temp_file = "/tmp/SYSCONF";
+  constexpr u32 SYSMENU_UID = 0x1000;
+  constexpr u16 SYSMENU_GID = 1;
+  constexpr auto rw_mode = IOS::HLE::FS::Mode::ReadWrite;
   {
-    File::IOFile file(temp_file, "wb");
-    if (!file.WriteBytes(buffer.data(), buffer.size()))
+    m_fs->CreateFile(SYSMENU_UID, SYSMENU_GID, temp_file, 0, rw_mode, rw_mode, rw_mode);
+    auto file = m_fs->OpenFile(SYSMENU_UID, SYSMENU_GID, temp_file, IOS::HLE::FS::Mode::Write);
+    if (!file || !file->Write(buffer.data(), buffer.size()))
       return false;
   }
-  return File::RenameSync(temp_file, m_file_name);
+  m_fs->CreateDirectory(SYSMENU_UID, SYSMENU_GID, "/shared2/sys", 0, rw_mode, rw_mode, rw_mode);
+  const auto result = m_fs->Rename(SYSMENU_UID, SYSMENU_GID, temp_file, "/shared2/sys/SYSCONF");
+  return result == IOS::HLE::FS::ResultCode::Success;
 }
 
 SysConf::Entry::Entry(Type type_, const std::string& name_) : type(type_), name(name_)
diff --git a/Source/Core/Common/SysConf.h b/Source/Core/Core/SysConf.h
similarity index 89%
rename from Source/Core/Common/SysConf.h
rename to Source/Core/Core/SysConf.h
index 92ff1c6718..241254e749 100644
--- a/Source/Core/Common/SysConf.h
+++ b/Source/Core/Core/SysConf.h
@@ -7,6 +7,7 @@
 #pragma once
 
 #include <cstring>
+#include <memory>
 #include <string>
 #include <vector>
 
@@ -14,10 +15,16 @@
 #include "Common/CommonTypes.h"
 #include "Common/NandPaths.h"
 
+namespace IOS::HLE::FS
+{
+class FileHandle;
+class FileSystem;
+}
+
 class SysConf final
 {
 public:
-  explicit SysConf(Common::FromWhichRoot root_type);
+  explicit SysConf(std::shared_ptr<IOS::HLE::FS::FileSystem> fs);
   ~SysConf();
 
   void Clear();
@@ -85,8 +92,8 @@ public:
 
 private:
   void InsertDefaultEntries();
-  bool LoadFromFile(const std::string& file_name);
+  bool LoadFromFile(const IOS::HLE::FS::FileHandle& file);
 
-  std::string m_file_name;
   std::vector<Entry> m_entries;
+  std::shared_ptr<IOS::HLE::FS::FileSystem> m_fs;
 };
diff --git a/Source/Core/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
index f6d696a435..a705801fc1 100644
--- a/Source/Core/Core/WiiRoot.cpp
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -11,10 +11,11 @@
 #include "Common/Logging/Log.h"
 #include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
-#include "Common/SysConf.h"
 #include "Core/ConfigManager.h"
+#include "Core/IOS/IOS.h"
 #include "Core/Movie.h"
 #include "Core/NetPlayClient.h"
+#include "Core/SysConf.h"
 
 namespace Core
 {
@@ -64,7 +65,7 @@ void InitializeWiiRoot(bool use_temporary)
     WARN_LOG(IOS_FS, "Using temporary directory %s for minimal Wii FS", s_temp_wii_root.c_str());
     File::SetUserPath(D_SESSION_WIIROOT_IDX, s_temp_wii_root);
     // Generate a SYSCONF with default settings for the temporary Wii NAND.
-    SysConf sysconf{Common::FromWhichRoot::FROM_SESSION_ROOT};
+    SysConf sysconf{IOS::HLE::Kernel{}.GetFS()};
     sysconf.Save();
 
     InitializeDeterministicWiiSaves();
diff --git a/Source/Core/Core/WiiUtils.cpp b/Source/Core/Core/WiiUtils.cpp
index 2c509cd5ca..931c400d4b 100644
--- a/Source/Core/Core/WiiUtils.cpp
+++ b/Source/Core/Core/WiiUtils.cpp
@@ -29,13 +29,13 @@
 #include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
 #include "Common/Swap.h"
-#include "Common/SysConf.h"
 #include "Core/CommonTitles.h"
 #include "Core/ConfigManager.h"
 #include "Core/IOS/Device.h"
 #include "Core/IOS/ES/ES.h"
 #include "Core/IOS/ES/Formats.h"
 #include "Core/IOS/IOS.h"
+#include "Core/SysConf.h"
 #include "DiscIO/DiscExtractor.h"
 #include "DiscIO/Enums.h"
 #include "DiscIO/Filesystem.h"
@@ -136,7 +136,7 @@ bool InstallWAD(IOS::HLE::Kernel& ios, const DiscIO::WiiWAD& wad, InstallType in
   }
 
   // Delete a previous temporary title, if it exists.
-  SysConf sysconf{Common::FROM_SESSION_ROOT};
+  SysConf sysconf{ios.GetFS()};
   SysConf::Entry* tid_entry = sysconf.GetOrAddEntry("IPL.TID", SysConf::Entry::Type::LongLong);
   if (const u64 previous_temporary_title_id = Common::swap64(tid_entry->GetData<u64>(0)))
     ios.GetES()->DeleteTitleContent(previous_temporary_title_id);
diff --git a/Source/Core/DolphinWX/GameListCtrl.cpp b/Source/Core/DolphinWX/GameListCtrl.cpp
index 6c893bccf3..c0f7303e90 100644
--- a/Source/Core/DolphinWX/GameListCtrl.cpp
+++ b/Source/Core/DolphinWX/GameListCtrl.cpp
@@ -39,7 +39,6 @@
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/StringUtil.h"
-#include "Common/SysConf.h"
 #include "Common/Thread.h"
 #include "Core/Boot/Boot.h"
 #include "Core/Config/NetplaySettings.h"
@@ -48,6 +47,7 @@
 #include "Core/HW/DVD/DVDInterface.h"
 #include "Core/HW/WiiSaveCrypted.h"
 #include "Core/Movie.h"
+#include "Core/SysConf.h"
 #include "Core/TitleDatabase.h"
 #include "Core/WiiUtils.h"
 #include "DiscIO/Blob.h"
diff --git a/Source/Core/DolphinWX/VideoConfigDiag.cpp b/Source/Core/DolphinWX/VideoConfigDiag.cpp
index ab9c983bb1..e3ad121d0c 100644
--- a/Source/Core/DolphinWX/VideoConfigDiag.cpp
+++ b/Source/Core/DolphinWX/VideoConfigDiag.cpp
@@ -24,10 +24,10 @@
 
 #include "Common/Assert.h"
 #include "Common/FileUtil.h"
-#include "Common/SysConf.h"
 #include "Core/Config/SYSCONFSettings.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
+#include "Core/SysConf.h"
 #include "DolphinWX/DolphinSlider.h"
 #include "DolphinWX/Frame.h"
 #include "DolphinWX/Main.h"