diff --git a/Source/Core/Common/SysConf.h → Source/Core/Core/SysConf.h b/Source/Core/Common/SysConf.h → Source/Core/Core/SysConf.h
@@ -7,17 +7,24 @@
 #pragma once
 
 #include <cstring>
+#include <memory>
 #include <string>
 #include <vector>
 
 #include "Common/Assert.h"
 #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 @@ class SysConf final
 
 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
@@ -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
@@ -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
@@ -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
@@ -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"