diff --git a/Source/Core/Common/FileUtil.cpp b/Source/Core/Common/FileUtil.cpp
index 19269e88d3..925e3f1ed3 100644
--- a/Source/Core/Common/FileUtil.cpp
+++ b/Source/Core/Common/FileUtil.cpp
@@ -20,6 +20,7 @@
 #include <commdlg.h>   // for GetSaveFileName
 #include <direct.h>    // getcwd
 #include <io.h>
+#include <objbase.h>   // guid stuff
 #include <shellapi.h>
 #include <windows.h>
 #else
@@ -666,6 +667,32 @@ bool SetCurrentDir(const std::string &directory)
 	return __chdir(directory.c_str()) == 0;
 }
 
+std::string CreateTempDir()
+{
+#ifdef _WIN32
+	TCHAR temp[MAX_PATH];
+	if (!GetTempPath(MAX_PATH, temp))
+		return "";
+
+	GUID guid;
+	CoCreateGuid(&guid);
+	TCHAR tguid[40];
+	StringFromGUID2(guid, tguid, 39);
+	tguid[39] = 0;
+	std::string dir = TStrToUTF8(temp) + "/" + TStrToUTF8(tguid);
+	if (!CreateDir(dir))
+		return "";
+	dir = ReplaceAll(dir, "\\", DIR_SEP);
+	return dir;
+#else
+	const char* base = getenv("TMPDIR") ?: "/tmp";
+	std::string path = std::string(base) + "/DolphinWii.XXXXXX";
+	if (!mkdtemp(&path[0]))
+		return "";
+	return path;
+#endif
+}
+
 std::string GetTempFilenameForAtomicWrite(const std::string &path)
 {
 	std::string abs = path;
@@ -734,17 +761,9 @@ static void RebuildUserDirectories(unsigned int dir_index)
 {
 	switch (dir_index)
 	{
-	case D_WIIROOT_IDX:
-		s_user_paths[D_WIIUSER_IDX]    = s_user_paths[D_WIIROOT_IDX] + DIR_SEP;
-		s_user_paths[D_WIISYSCONF_IDX] = s_user_paths[D_WIIUSER_IDX] + WII_SYSCONF_DIR + DIR_SEP;
-		s_user_paths[D_WIIWC24_IDX]    = s_user_paths[D_WIIUSER_IDX] + WII_WC24CONF_DIR DIR_SEP;
-		s_user_paths[F_WIISYSCONF_IDX] = s_user_paths[D_WIISYSCONF_IDX] + WII_SYSCONF;
-		break;
-
 	case D_USER_IDX:
 		s_user_paths[D_GCUSER_IDX]         = s_user_paths[D_USER_IDX] + GC_USER_DIR DIR_SEP;
 		s_user_paths[D_WIIROOT_IDX]        = s_user_paths[D_USER_IDX] + WII_USER_DIR;
-		s_user_paths[D_WIIUSER_IDX]        = s_user_paths[D_WIIROOT_IDX] + DIR_SEP;
 		s_user_paths[D_CONFIG_IDX]         = s_user_paths[D_USER_IDX] + CONFIG_DIR DIR_SEP;
 		s_user_paths[D_GAMESETTINGS_IDX]   = s_user_paths[D_USER_IDX] + GAMESETTINGS_DIR DIR_SEP;
 		s_user_paths[D_MAPS_IDX]           = s_user_paths[D_USER_IDX] + MAPS_DIR DIR_SEP;
@@ -762,14 +781,11 @@ static void RebuildUserDirectories(unsigned int dir_index)
 		s_user_paths[D_DUMPDSP_IDX]        = s_user_paths[D_DUMP_IDX] + DUMP_DSP_DIR DIR_SEP;
 		s_user_paths[D_LOGS_IDX]           = s_user_paths[D_USER_IDX] + LOGS_DIR DIR_SEP;
 		s_user_paths[D_MAILLOGS_IDX]       = s_user_paths[D_LOGS_IDX] + MAIL_LOGS_DIR DIR_SEP;
-		s_user_paths[D_WIISYSCONF_IDX]     = s_user_paths[D_WIIUSER_IDX] + WII_SYSCONF_DIR DIR_SEP;
-		s_user_paths[D_WIIWC24_IDX]    = s_user_paths[D_WIIUSER_IDX] + WII_WC24CONF_DIR DIR_SEP;
 		s_user_paths[D_THEMES_IDX]         = s_user_paths[D_USER_IDX] + THEMES_DIR DIR_SEP;
 		s_user_paths[F_DOLPHINCONFIG_IDX]  = s_user_paths[D_CONFIG_IDX] + DOLPHIN_CONFIG;
 		s_user_paths[F_DEBUGGERCONFIG_IDX] = s_user_paths[D_CONFIG_IDX] + DEBUGGER_CONFIG;
 		s_user_paths[F_LOGGERCONFIG_IDX]   = s_user_paths[D_CONFIG_IDX] + LOGGER_CONFIG;
 		s_user_paths[F_MAINLOG_IDX]        = s_user_paths[D_LOGS_IDX] + MAIN_LOG;
-		s_user_paths[F_WIISYSCONF_IDX]     = s_user_paths[D_WIISYSCONF_IDX] + WII_SYSCONF;
 		s_user_paths[F_RAMDUMP_IDX]        = s_user_paths[D_DUMP_IDX] + RAM_DUMP;
 		s_user_paths[F_ARAMDUMP_IDX]       = s_user_paths[D_DUMP_IDX] + ARAM_DUMP;
 		s_user_paths[F_FAKEVMEMDUMP_IDX]   = s_user_paths[D_DUMP_IDX] + FAKEVMEM_DUMP;
diff --git a/Source/Core/Common/FileUtil.h b/Source/Core/Common/FileUtil.h
index 3ad7b08d5b..1337ee1670 100644
--- a/Source/Core/Common/FileUtil.h
+++ b/Source/Core/Common/FileUtil.h
@@ -20,8 +20,8 @@
 enum {
 	D_USER_IDX,
 	D_GCUSER_IDX,
-	D_WIIROOT_IDX,
-	D_WIIUSER_IDX,
+	D_WIIROOT_IDX, // always points to User/Wii or global user-configured directory
+	D_SESSION_WIIROOT_IDX, // may point to minimal temporary directory for determinism
 	D_CONFIG_IDX, // global settings
 	D_GAMESETTINGS_IDX, // user-specified settings which override both the global and the default settings (per game)
 	D_MAPS_IDX,
@@ -39,14 +39,11 @@ enum {
 	D_LOAD_IDX,
 	D_LOGS_IDX,
 	D_MAILLOGS_IDX,
-	D_WIISYSCONF_IDX,
-	D_WIIWC24_IDX,
 	D_THEMES_IDX,
 	F_DOLPHINCONFIG_IDX,
 	F_DEBUGGERCONFIG_IDX,
 	F_LOGGERCONFIG_IDX,
 	F_MAINLOG_IDX,
-	F_WIISYSCONF_IDX,
 	F_RAMDUMP_IDX,
 	F_ARAMDUMP_IDX,
 	F_FAKEVMEMDUMP_IDX,
@@ -122,6 +119,9 @@ void CopyDir(const std::string &source_path, const std::string &dest_path);
 // Set the current directory to given directory
 bool SetCurrentDir(const std::string &directory);
 
+// Creates and returns the path to a new temporary directory.
+std::string CreateTempDir();
+
 // Get a filename that can hopefully be atomically renamed to the given path.
 std::string GetTempFilenameForAtomicWrite(const std::string &path);
 
diff --git a/Source/Core/Common/NandPaths.cpp b/Source/Core/Common/NandPaths.cpp
index c695d0744a..6037137410 100644
--- a/Source/Core/Common/NandPaths.cpp
+++ b/Source/Core/Common/NandPaths.cpp
@@ -7,6 +7,7 @@
 #include <string>
 #include <utility>
 
+#include "Common/CommonPaths.h"
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/NandPaths.h"
@@ -15,17 +16,55 @@
 namespace Common
 {
 
+static std::string s_temp_wii_root;
+
+void InitializeWiiRoot(bool use_dummy)
+{
+	ShutdownWiiRoot();
+	if (use_dummy)
+	{
+		s_temp_wii_root = File::CreateTempDir();
+		if (s_temp_wii_root.empty())
+		{
+			ERROR_LOG(WII_IPC_FILEIO, "Could not create temporary directory");
+			return;
+		}
+		File::CopyDir(File::GetSysDirectory() + WII_USER_DIR, s_temp_wii_root);
+		WARN_LOG(WII_IPC_FILEIO, "Using temporary directory %s for minimal Wii FS", s_temp_wii_root.c_str());
+		static bool s_registered;
+		if (!s_registered)
+		{
+			s_registered = true;
+			atexit(ShutdownWiiRoot);
+		}
+		File::SetUserPath(D_SESSION_WIIROOT_IDX, s_temp_wii_root);
+	}
+	else
+	{
+		File::SetUserPath(D_SESSION_WIIROOT_IDX, File::GetUserPath(D_WIIROOT_IDX));
+	}
+}
+
+void ShutdownWiiRoot()
+{
+	if (!s_temp_wii_root.empty())
+	{
+		File::DeleteDirRecursively(s_temp_wii_root);
+		s_temp_wii_root.clear();
+	}
+}
+
 std::string GetTicketFileName(u64 _titleID)
 {
-	return StringFromFormat("%sticket/%08x/%08x.tik",
-			File::GetUserPath(D_WIIUSER_IDX).c_str(),
+	return StringFromFormat("%s/ticket/%08x/%08x.tik",
+			File::GetUserPath(D_SESSION_WIIROOT_IDX).c_str(),
 			(u32)(_titleID >> 32), (u32)_titleID);
 }
 
 std::string GetTitleDataPath(u64 _titleID)
 {
-	return StringFromFormat("%stitle/%08x/%08x/data/",
-			File::GetUserPath(D_WIIUSER_IDX).c_str(),
+	return StringFromFormat("%s/title/%08x/%08x/data/",
+			File::GetUserPath(D_SESSION_WIIROOT_IDX).c_str(),
 			(u32)(_titleID >> 32), (u32)_titleID);
 }
 
@@ -35,8 +74,8 @@ std::string GetTMDFileName(u64 _titleID)
 }
 std::string GetTitleContentPath(u64 _titleID)
 {
-	return StringFromFormat("%stitle/%08x/%08x/content/",
-			File::GetUserPath(D_WIIUSER_IDX).c_str(),
+	return StringFromFormat("%s/title/%08x/%08x/content/",
+			File::GetUserPath(D_SESSION_WIIROOT_IDX).c_str(),
 			(u32)(_titleID >> 32), (u32)_titleID);
 }
 
@@ -89,8 +128,7 @@ void ReadReplacements(replace_v& replacements)
 {
 	replacements.clear();
 	const std::string replace_fname = "/sys/replace";
-	std::string filename(File::GetUserPath(D_WIIROOT_IDX));
-	filename += replace_fname;
+	std::string filename = File::GetUserPath(D_SESSION_WIIROOT_IDX) + replace_fname;
 
 	if (!File::Exists(filename))
 		CreateReplacementFile(filename);
diff --git a/Source/Core/Common/NandPaths.h b/Source/Core/Common/NandPaths.h
index 4adfed131f..6a79abf3bf 100644
--- a/Source/Core/Common/NandPaths.h
+++ b/Source/Core/Common/NandPaths.h
@@ -18,6 +18,9 @@ namespace Common
 	typedef std::pair<char, std::string> replace_t;
 	typedef std::vector<replace_t> replace_v;
 
+	void InitializeWiiRoot(bool use_temporary);
+	void ShutdownWiiRoot();
+
 	std::string GetTicketFileName(u64 _titleID);
 	std::string GetTMDFileName(u64 _titleID);
 	std::string GetTitleDataPath(u64 _titleID);
diff --git a/Source/Core/Common/SysConf.cpp b/Source/Core/Common/SysConf.cpp
index 94124c4957..a0d3aa1f04 100644
--- a/Source/Core/Common/SysConf.cpp
+++ b/Source/Core/Common/SysConf.cpp
@@ -8,6 +8,7 @@
 #include <string>
 #include <vector>
 
+#include "Common/CommonPaths.h"
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/SysConf.h"
@@ -15,8 +16,7 @@
 SysConf::SysConf()
 	: m_IsValid(false)
 {
-	m_FilenameDefault = File::GetUserPath(F_WIISYSCONF_IDX);
-	m_IsValid = LoadFromFile(m_FilenameDefault);
+	UpdateLocation();
 }
 
 SysConf::~SysConf()
@@ -409,7 +409,10 @@ void SysConf::UpdateLocation()
 	// Clear the old filename and set the default filename to the new user path
 	// So that it can be generated if the file does not exist in the new location
 	m_Filename.clear();
-	m_FilenameDefault =  File::GetUserPath(F_WIISYSCONF_IDX);
+	// Note: We don't use the dummy Wii root here (if in use) because this is
+	// all tied up with the configuration code.  In the future this should
+	// probably just be synced with the other settings.
+	m_FilenameDefault = File::GetUserPath(D_WIIROOT_IDX) + DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF;
 	Reload();
 }
 
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index a06cc48839..81a85c5063 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -475,8 +475,6 @@ void SConfig::LoadGeneralSettings(IniFile& ini)
 
 	general->Get("NANDRootPath", &m_NANDPath);
 	File::SetUserPath(D_WIIROOT_IDX, m_NANDPath);
-	DiscIO::cUIDsys::AccessInstance().UpdateLocation();
-	DiscIO::CSharedContent::AccessInstance().UpdateLocation();
 	general->Get("WirelessMac", &m_WirelessMac);
 }
 
diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 2972760d34..449682e051 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -832,6 +832,7 @@ void UpdateWantDeterminism(bool initial)
 		g_video_backend->UpdateWantDeterminism(new_want_determinism);
 		// We need to clear the cache because some parts of the JIT depend on want_determinism, e.g. use of FMA.
 		JitInterface::ClearCache();
+		Common::InitializeWiiRoot(g_want_determinism);
 
 		Core::PauseAndLock(false, was_unpaused);
 	}
diff --git a/Source/Core/Core/HW/HW.cpp b/Source/Core/Core/HW/HW.cpp
index ef0aee3a85..533c392cf5 100644
--- a/Source/Core/Core/HW/HW.cpp
+++ b/Source/Core/Core/HW/HW.cpp
@@ -4,6 +4,7 @@
 
 #include "Common/ChunkFile.h"
 #include "Common/CommonTypes.h"
+#include "Common/NandPaths.h"
 
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
@@ -25,6 +26,7 @@
 #include "Core/IPC_HLE/WII_IPC_HLE.h"
 #include "Core/PowerPC/PowerPC.h"
 #include "Core/PowerPC/PPCAnalyst.h"
+#include "DiscIO/NANDContentLoader.h"
 
 namespace HW
 {
@@ -50,6 +52,9 @@ namespace HW
 
 		if (SConfig::GetInstance().m_LocalCoreStartupParameter.bWii)
 		{
+			Common::InitializeWiiRoot(Core::g_want_determinism);
+			DiscIO::cUIDsys::AccessInstance().UpdateLocation();
+			DiscIO::CSharedContent::AccessInstance().UpdateLocation();
 			WII_IPCInterface::Init();
 			WII_IPC_HLE_Interface::Init();
 		}
@@ -70,6 +75,7 @@ namespace HW
 		{
 			WII_IPCInterface::Shutdown();
 			WII_IPC_HLE_Interface::Shutdown();
+			Common::ShutdownWiiRoot();
 		}
 
 		State::Shutdown();
diff --git a/Source/Core/Core/HW/WiiSaveCrypted.cpp b/Source/Core/Core/HW/WiiSaveCrypted.cpp
index 4d50fcaa21..beae07402d 100644
--- a/Source/Core/Core/HW/WiiSaveCrypted.cpp
+++ b/Source/Core/Core/HW/WiiSaveCrypted.cpp
@@ -62,7 +62,7 @@ bool CWiiSaveCrypted::ExportWiiSave(u64 title_id)
 
 void CWiiSaveCrypted::ExportAllSaves()
 {
-	std::string title_folder = File::GetUserPath(D_WIIUSER_IDX) + "title";
+	std::string title_folder = File::GetUserPath(D_WIIROOT_IDX) + "/title";
 	std::vector<u64> titles;
 	const u32 path_mask = 0x00010000;
 	for (int i = 0; i < 8; ++i)
diff --git a/Source/Core/Core/HW/WiimoteEmu/EmuSubroutines.cpp b/Source/Core/Core/HW/WiimoteEmu/EmuSubroutines.cpp
index feaa0c82b0..d075d8a192 100644
--- a/Source/Core/Core/HW/WiimoteEmu/EmuSubroutines.cpp
+++ b/Source/Core/Core/HW/WiimoteEmu/EmuSubroutines.cpp
@@ -22,6 +22,7 @@
 
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
+#include "Common/NandPaths.h"
 
 #include "Core/HW/WiimoteEmu/WiimoteEmu.h"
 #include "Core/HW/WiimoteEmu/WiimoteHid.h"
@@ -275,7 +276,7 @@ void Wiimote::WriteData(const wm_write_data* const wd)
 			{
 				// writing the whole mii block each write :/
 				std::ofstream file;
-				OpenFStream(file, File::GetUserPath(D_WIIUSER_IDX) + "mii.bin", std::ios::binary | std::ios::out);
+				OpenFStream(file, File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/mii.bin", std::ios::binary | std::ios::out);
 				file.write((char*)m_eeprom + 0x0FCA, 0x02f0);
 				file.close();
 			}
@@ -417,7 +418,7 @@ void Wiimote::ReadData(const wm_read_data* const rd)
 			{
 				// reading the whole mii block :/
 				std::ifstream file;
-				file.open((File::GetUserPath(D_WIIUSER_IDX) + "mii.bin").c_str(), std::ios::binary | std::ios::in);
+				file.open((File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/mii.bin").c_str(), std::ios::binary | std::ios::in);
 				file.read((char*)m_eeprom + 0x0FCA, 0x02f0);
 				file.close();
 			}
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_FileIO.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_FileIO.cpp
index c14186f6f0..5e300ce120 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_FileIO.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_FileIO.cpp
@@ -5,11 +5,14 @@
 #include <algorithm>
 
 #include "Common/ChunkFile.h"
+#include "Common/CommonPaths.h"
 #include "Common/CommonTypes.h"
 #include "Common/FileUtil.h"
 #include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
 
+#include "Core/Core.h"
+#include "Core/IPC_HLE/WII_IPC_HLE.h"
 #include "Core/IPC_HLE/WII_IPC_HLE_Device_FileIO.h"
 #include "Core/IPC_HLE/WII_IPC_HLE_Device_fs.h"
 
@@ -19,7 +22,7 @@ static Common::replace_v replacements;
 // This is used by several of the FileIO and /dev/fs functions
 std::string HLE_IPC_BuildFilename(std::string path_wii)
 {
-	std::string path_full = File::GetUserPath(D_WIIROOT_IDX);
+	std::string path_full = File::GetUserPath(D_SESSION_WIIROOT_IDX);
 
 	// Replaces chars that FAT32 can't support with strings defined in /sys/replace
 	for (auto& replacement : replacements)
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_fs.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_fs.cpp
index 70368267f8..68108705fb 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_fs.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_fs.cpp
@@ -32,7 +32,7 @@ IPCCommandResult CWII_IPC_HLE_Device_fs::Open(u32 _CommandAddress, u32 _Mode)
 {
 	// clear tmp folder
 	{
-		std::string Path = File::GetUserPath(D_WIIUSER_IDX) + "tmp";
+		std::string Path = HLE_IPC_BuildFilename("/tmp");
 		File::DeleteDirRecursively(Path);
 		File::CreateDir(Path);
 	}
@@ -221,7 +221,6 @@ IPCCommandResult CWII_IPC_HLE_Device_fs::IOCtlV(u32 _CommandAddress)
 IPCCommandResult CWII_IPC_HLE_Device_fs::IOCtl(u32 _CommandAddress)
 {
 	//u32 DeviceID = Memory::Read_U32(_CommandAddress + 8);
-	//LOG(WII_IPC_FILEIO, "FS: IOCtl (Device=%s, DeviceID=%08x)", GetDeviceName().c_str(), DeviceID);
 
 	u32 Parameter =  Memory::Read_U32(_CommandAddress + 0xC);
 	u32 BufferIn =  Memory::Read_U32(_CommandAddress + 0x10);
@@ -483,7 +482,7 @@ void CWII_IPC_HLE_Device_fs::DoState(PointerWrap& p)
 
 	// handle /tmp
 
-	std::string Path = File::GetUserPath(D_WIIUSER_IDX) + "tmp";
+	std::string Path = File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/tmp";
 	if (p.GetMode() == PointerWrap::MODE_READ)
 	{
 		File::DeleteDirRecursively(Path);
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net.h b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net.h
index b06b45f7d0..c1cecee67e 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net.h
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net.h
@@ -4,7 +4,9 @@
 
 #pragma once
 
+#include "Common/CommonPaths.h"
 #include "Common/FileUtil.h"
+#include "Common/NandPaths.h"
 #include "Common/Timer.h"
 
 #include "Core/HW/EXI_DeviceIPL.h"
@@ -172,7 +174,7 @@ private:
 public:
 	NWC24Config()
 	{
-		path = File::GetUserPath(D_WIIWC24_IDX) + "nwc24msg.cfg";
+		path = File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/" WII_WC24CONF_DIR "/nwc24msg.cfg";
 		ReadConfig();
 	}
 
@@ -211,7 +213,7 @@ public:
 	{
 		if (!File::Exists(path))
 		{
-			if (!File::CreateFullPath(File::GetUserPath(D_WIIWC24_IDX)))
+			if (!File::CreateFullPath(File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/" WII_WC24CONF_DIR))
 			{
 				ERROR_LOG(WII_IPC_WC24, "Failed to create directory for WC24");
 			}
@@ -322,7 +324,7 @@ class WiiNetConfig
 public:
 	WiiNetConfig()
 	{
-		path = File::GetUserPath(D_WIISYSCONF_IDX) + "net/02/config.dat";
+		path = File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/" WII_SYSCONF_DIR "/net/02/config.dat";
 		ReadConfig();
 	}
 
@@ -347,7 +349,7 @@ public:
 	{
 		if (!File::Exists(path))
 		{
-			if (!File::CreateFullPath(std::string(File::GetUserPath(D_WIISYSCONF_IDX) + "net/02/")))
+			if (!File::CreateFullPath(std::string(File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/" WII_SYSCONF_DIR "/net/02/")))
 			{
 				ERROR_LOG(WII_IPC_NET, "Failed to create directory for network config file");
 			}
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net_ssl.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net_ssl.cpp
index 456e181960..03c50a97ce 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net_ssl.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_net_ssl.cpp
@@ -5,6 +5,7 @@
 #include <algorithm>
 
 #include "Common/FileUtil.h"
+#include "Common/NandPaths.h"
 #include "Core/Core.h"
 #include "Core/IPC_HLE/WII_IPC_HLE_Device_net_ssl.h"
 #include "Core/IPC_HLE/WII_Socket.h"
@@ -286,7 +287,7 @@ _SSL_NEW_ERROR:
 		if (SSLID_VALID(sslID))
 		{
 			WII_SSL* ssl = &_SSL[sslID];
-			std::string cert_base_path(File::GetUserPath(D_WIIUSER_IDX));
+			std::string cert_base_path = File::GetUserPath(D_SESSION_WIIROOT_IDX);
 			int ret = x509_crt_parse_file(&ssl->clicert, (cert_base_path + "clientca.pem").c_str());
 			int pk_ret = pk_parse_keyfile(&ssl->pk, (cert_base_path + "clientcakey.pem").c_str(), nullptr);
 			if (ret || pk_ret)
@@ -343,9 +344,8 @@ _SSL_NEW_ERROR:
 		if (SSLID_VALID(sslID))
 		{
 			WII_SSL* ssl = &_SSL[sslID];
-			std::string cert_base_path(File::GetUserPath(D_WIIUSER_IDX));
 
-			int ret = x509_crt_parse_file(&ssl->cacert, (cert_base_path + "rootca.pem").c_str());
+			int ret = x509_crt_parse_file(&ssl->cacert, (File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/rootca.pem").c_str());
 			if (ret)
 			{
 				x509_crt_free(&ssl->clicert);
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_sdio_slot0.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_sdio_slot0.cpp
index c2bb9c9fe8..b4e3f149db 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_sdio_slot0.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_sdio_slot0.cpp
@@ -61,7 +61,7 @@ void CWII_IPC_HLE_Device_sdio_slot0::EventNotify()
 
 void CWII_IPC_HLE_Device_sdio_slot0::OpenInternal()
 {
-	const std::string filename = File::GetUserPath(D_WIIUSER_IDX) + "sd.raw";
+	const std::string filename = File::GetUserPath(D_WIIROOT_IDX) + "/sd.raw";
 	m_Card.Open(filename, "r+b");
 	if (!m_Card)
 	{
diff --git a/Source/Core/Core/ec_wii.cpp b/Source/Core/Core/ec_wii.cpp
index 272aacac8c..d786d8fe75 100644
--- a/Source/Core/Core/ec_wii.cpp
+++ b/Source/Core/Core/ec_wii.cpp
@@ -119,7 +119,7 @@ void make_blanksig_ec_cert(u8 *cert_out, const char *signer, const char *name, c
 EcWii::EcWii()
 {
 	bool init = true;
-	std::string keys_path = File::GetUserPath(D_WIIUSER_IDX) + "keys.bin";
+	std::string keys_path = File::GetUserPath(D_WIIROOT_IDX) + "/keys.bin";
 	if (File::Exists(keys_path))
 	{
 		File::IOFile keys_f(keys_path, "rb");
diff --git a/Source/Core/DiscIO/NANDContentLoader.cpp b/Source/Core/DiscIO/NANDContentLoader.cpp
index 715ac6e878..c247713ee3 100644
--- a/Source/Core/DiscIO/NANDContentLoader.cpp
+++ b/Source/Core/DiscIO/NANDContentLoader.cpp
@@ -35,7 +35,7 @@ void CSharedContent::UpdateLocation()
 {
 	m_Elements.clear();
 	m_lastID = 0;
-	m_contentMap = StringFromFormat("%sshared1/content.map", File::GetUserPath(D_WIIUSER_IDX).c_str());
+	m_contentMap = StringFromFormat("%s/shared1/content.map", File::GetUserPath(D_WIIROOT_IDX).c_str());
 
 	File::IOFile pFile(m_contentMap, "rb");
 	SElement Element;
@@ -55,7 +55,7 @@ std::string CSharedContent::GetFilenameFromSHA1(const u8* _pHash)
 	{
 		if (memcmp(_pHash, Element.SHA1Hash, 20) == 0)
 		{
-			return StringFromFormat("%sshared1/%c%c%c%c%c%c%c%c.app", File::GetUserPath(D_WIIUSER_IDX).c_str(),
+			return StringFromFormat("%s/shared1/%c%c%c%c%c%c%c%c.app", File::GetUserPath(D_WIIROOT_IDX).c_str(),
 			    Element.FileName[0], Element.FileName[1], Element.FileName[2], Element.FileName[3],
 			    Element.FileName[4], Element.FileName[5], Element.FileName[6], Element.FileName[7]);
 		}
@@ -80,7 +80,7 @@ std::string CSharedContent::AddSharedContent(const u8* _pHash)
 		File::IOFile pFile(m_contentMap, "ab");
 		pFile.WriteArray(&Element, 1);
 
-		filename = StringFromFormat("%sshared1/%s.app", File::GetUserPath(D_WIIUSER_IDX).c_str(), id.c_str());
+		filename = StringFromFormat("%s/shared1/%s.app", File::GetUserPath(D_WIIROOT_IDX).c_str(), id.c_str());
 		m_lastID++;
 	}
 
@@ -371,7 +371,7 @@ void cUIDsys::UpdateLocation()
 {
 	m_Elements.clear();
 	m_lastUID = 0x00001000;
-	m_uidSys = StringFromFormat("%ssys/uid.sys", File::GetUserPath(D_WIIUSER_IDX).c_str());
+	m_uidSys = File::GetUserPath(D_SESSION_WIIROOT_IDX) + "/sys/uid.sys";
 
 	File::IOFile pFile(m_uidSys, "rb");
 	SElement Element;
diff --git a/Source/Core/DiscIO/VolumeCommon.cpp b/Source/Core/DiscIO/VolumeCommon.cpp
index cb4386af68..6d3998d85c 100644
--- a/Source/Core/DiscIO/VolumeCommon.cpp
+++ b/Source/Core/DiscIO/VolumeCommon.cpp
@@ -33,8 +33,8 @@ std::vector<u32> IVolume::GetBanner(int* width, int* height) const
 	GetTitleID((u8*)&TitleID);
 	TitleID = Common::swap64(TitleID);
 
-	std::string file_name = StringFromFormat("%stitle/%08x/%08x/data/banner.bin",
-		File::GetUserPath(D_WIIUSER_IDX).c_str(), (u32)(TitleID >> 32), (u32)TitleID);
+	std::string file_name = StringFromFormat("%s/title/%08x/%08x/data/banner.bin",
+		File::GetUserPath(D_WIIROOT_IDX).c_str(), (u32)(TitleID >> 32), (u32)TitleID);
 	if (!File::Exists(file_name))
 		return std::vector<u32>();
 
diff --git a/Source/Core/DolphinQt/GameList/GameFile.cpp b/Source/Core/DolphinQt/GameList/GameFile.cpp
index e8cbe83f3c..b7ee748c52 100644
--- a/Source/Core/DolphinQt/GameList/GameFile.cpp
+++ b/Source/Core/DolphinQt/GameList/GameFile.cpp
@@ -292,7 +292,7 @@ const QString GameFile::GetWiiFSPath() const
 		volume->GetTitleID((u8*)&title);
 		title = Common::swap64(title);
 
-		path = StringFromFormat("%stitle/%08x/%08x/data/", File::GetUserPath(D_WIIUSER_IDX).c_str(), (u32)(title >> 32), (u32)title);
+		path = StringFromFormat("%s/title/%08x/%08x/data/", File::GetUserPath(D_WIIROOT_IDX).c_str(), (u32)(title >> 32), (u32)title);
 
 		if (!File::Exists(path))
 			File::CreateFullPath(path);
diff --git a/Source/Core/DolphinWX/Config/PathConfigPane.cpp b/Source/Core/DolphinWX/Config/PathConfigPane.cpp
index 04e9f20aab..efde03d64d 100644
--- a/Source/Core/DolphinWX/Config/PathConfigPane.cpp
+++ b/Source/Core/DolphinWX/Config/PathConfigPane.cpp
@@ -182,8 +182,6 @@ void PathConfigPane::OnNANDRootChanged(wxCommandEvent& event)
 	m_nand_root_dirpicker->SetPath(StrToWxStr(nand_path));
 
 	SConfig::GetInstance().m_SYSCONF->UpdateLocation();
-	DiscIO::cUIDsys::AccessInstance().UpdateLocation();
-	DiscIO::CSharedContent::AccessInstance().UpdateLocation();
 
 	main_frame->UpdateWiiMenuChoice();
 }
diff --git a/Source/Core/DolphinWX/ISOFile.cpp b/Source/Core/DolphinWX/ISOFile.cpp
index a85586e7d5..f4b05a855c 100644
--- a/Source/Core/DolphinWX/ISOFile.cpp
+++ b/Source/Core/DolphinWX/ISOFile.cpp
@@ -259,8 +259,8 @@ const std::string GameListItem::GetWiiFSPath() const
 		iso->GetTitleID((u8*)&title);
 		title = Common::swap64(title);
 
-		const std::string path = StringFromFormat("%stitle/%08x/%08x/data/",
-				File::GetUserPath(D_WIIUSER_IDX).c_str(), (u32)(title>>32), (u32)title);
+		const std::string path = StringFromFormat("%s/title/%08x/%08x/data/",
+				File::GetUserPath(D_WIIROOT_IDX).c_str(), (u32)(title>>32), (u32)title);
 
 		if (!File::Exists(path))
 			File::CreateFullPath(path);
diff --git a/Source/Core/DolphinWX/MainAndroid.cpp b/Source/Core/DolphinWX/MainAndroid.cpp
index 2f37f36240..95b816c50b 100644
--- a/Source/Core/DolphinWX/MainAndroid.cpp
+++ b/Source/Core/DolphinWX/MainAndroid.cpp
@@ -537,7 +537,7 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_CreateUserFo
 {
 	File::CreateFullPath(File::GetUserPath(D_CONFIG_IDX));
 	File::CreateFullPath(File::GetUserPath(D_GCUSER_IDX));
-	File::CreateFullPath(File::GetUserPath(D_WIIUSER_IDX));
+	File::CreateFullPath(File::GetUserPath(D_WIIROOT_IDX) + DIR_SEP);
 	File::CreateFullPath(File::GetUserPath(D_CACHE_IDX));
 	File::CreateFullPath(File::GetUserPath(D_DUMPDSP_IDX));
 	File::CreateFullPath(File::GetUserPath(D_DUMPTEXTURES_IDX));
diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
index f1fa25ff44..a8394d9ea4 100644
--- a/Source/Core/UICommon/UICommon.cpp
+++ b/Source/Core/UICommon/UICommon.cpp
@@ -51,8 +51,8 @@ void Shutdown()
 void CreateDirectories()
 {
 	// Copy initial Wii NAND data from Sys to User.
-	File::CopyDir(File::GetSysDirectory() + WII_USER_DIR DIR_SEP,
-				  File::GetUserPath(D_WIIUSER_IDX));
+	File::CopyDir(File::GetSysDirectory() + WII_USER_DIR,
+				  File::GetUserPath(D_WIIROOT_IDX));
 
 	File::CreateFullPath(File::GetUserPath(D_USER_IDX));
 	File::CreateFullPath(File::GetUserPath(D_CACHE_IDX));