diff --git a/Source/Core/Common/SysConf.cpp b/Source/Core/Common/SysConf.cpp
index 22e902d042..36ab4fa325 100644
--- a/Source/Core/Common/SysConf.cpp
+++ b/Source/Core/Common/SysConf.cpp
@@ -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/Common/SysConf.h
index 92ff1c6718..241254e749 100644
--- a/Source/Core/Common/SysConf.h
+++ b/Source/Core/Common/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/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index 4dcfb613ae..b652aa922b 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -22,6 +22,7 @@
 #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"
 
 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/IOS/USB/Bluetooth/BTEmu.cpp b/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp
index 11b0da139e..e98fb9f35f 100644
--- a/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp
+++ b/Source/Core/Core/IOS/USB/Bluetooth/BTEmu.cpp
@@ -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/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
index f6d696a435..cb87cc6dec 100644
--- a/Source/Core/Core/WiiRoot.cpp
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -13,6 +13,7 @@
 #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"
 
@@ -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..91538a5bef 100644
--- a/Source/Core/Core/WiiUtils.cpp
+++ b/Source/Core/Core/WiiUtils.cpp
@@ -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);