diff --git a/Source/Core/Common/Config/Config.cpp b/Source/Core/Common/Config/Config.cpp
index 7e1fc904d9..30215aec06 100644
--- a/Source/Core/Common/Config/Config.cpp
+++ b/Source/Core/Common/Config/Config.cpp
@@ -62,12 +62,14 @@ void Load()
 {
   for (auto& layer : s_layers)
     layer.second->Load();
+  InvokeConfigChangedCallbacks();
 }
 
 void Save()
 {
   for (auto& layer : s_layers)
     layer.second->Save();
+  InvokeConfigChangedCallbacks();
 }
 
 void Init()
diff --git a/Source/Core/Common/Config/Layer.cpp b/Source/Core/Common/Config/Layer.cpp
index 5a5c4b5f59..6653dbfe65 100644
--- a/Source/Core/Common/Config/Layer.cpp
+++ b/Source/Core/Common/Config/Layer.cpp
@@ -115,7 +115,6 @@ void Layer::Load()
   if (m_loader)
     m_loader->Load(this);
   m_is_dirty = false;
-  InvokeConfigChangedCallbacks();
 }
 
 void Layer::Save()
@@ -125,7 +124,6 @@ void Layer::Save()
 
   m_loader->Save(this);
   m_is_dirty = false;
-  InvokeConfigChangedCallbacks();
 }
 
 LayerType Layer::GetLayer() const
diff --git a/Source/Core/Core/Config/MainSettings.cpp b/Source/Core/Core/Config/MainSettings.cpp
index 77687c28df..9f4811bdb3 100644
--- a/Source/Core/Core/Config/MainSettings.cpp
+++ b/Source/Core/Core/Config/MainSettings.cpp
@@ -106,4 +106,10 @@ const ConfigInfo<std::string> MAIN_AUDIO_BACKEND{{System::Main, "DSP", "Backend"
                                                  AudioCommon::GetDefaultSoundBackend()};
 const ConfigInfo<int> MAIN_AUDIO_VOLUME{{System::Main, "DSP", "Volume"}, 100};
 
+// Main.General
+
+const ConfigInfo<std::string> MAIN_DUMP_PATH{{System::Main, "General", "DumpPath"}, ""};
+const ConfigInfo<std::string> MAIN_FS_PATH{{System::Main, "General", "NANDRootPath"}, ""};
+const ConfigInfo<std::string> MAIN_SD_PATH{{System::Main, "General", "WiiSDCardPath"}, ""};
+
 }  // namespace Config
diff --git a/Source/Core/Core/Config/MainSettings.h b/Source/Core/Core/Config/MainSettings.h
index 871e103bb9..ab99f889d7 100644
--- a/Source/Core/Core/Config/MainSettings.h
+++ b/Source/Core/Core/Config/MainSettings.h
@@ -78,4 +78,10 @@ extern const ConfigInfo<bool> MAIN_DUMP_UCODE;
 extern const ConfigInfo<std::string> MAIN_AUDIO_BACKEND;
 extern const ConfigInfo<int> MAIN_AUDIO_VOLUME;
 
+// Main.General
+
+extern const ConfigInfo<std::string> MAIN_DUMP_PATH;
+extern const ConfigInfo<std::string> MAIN_FS_PATH;
+extern const ConfigInfo<std::string> MAIN_SD_PATH;
+
 }  // namespace Config
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index 0518a6d400..e7c4f42e0f 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -98,21 +98,6 @@ void SConfig::SaveSettings()
   Config::Save();
 }
 
-namespace
-{
-void CreateDumpPath(const std::string& path)
-{
-  if (path.empty())
-    return;
-  File::SetUserPath(D_DUMP_IDX, path + '/');
-  File::CreateFullPath(File::GetUserPath(D_DUMPAUDIO_IDX));
-  File::CreateFullPath(File::GetUserPath(D_DUMPDSP_IDX));
-  File::CreateFullPath(File::GetUserPath(D_DUMPSSL_IDX));
-  File::CreateFullPath(File::GetUserPath(D_DUMPFRAMES_IDX));
-  File::CreateFullPath(File::GetUserPath(D_DUMPTEXTURES_IDX));
-}
-}  // namespace
-
 void SConfig::SaveGeneralSettings(IniFile& ini)
 {
   IniFile::Section* general = ini.GetOrCreateSection("General");
@@ -138,11 +123,7 @@ void SConfig::SaveGeneralSettings(IniFile& ini)
   }
 
   general->Set("RecursiveISOPaths", m_RecursiveISOFolder);
-  general->Set("NANDRootPath", m_NANDPath);
-  general->Set("DumpPath", m_DumpPath);
-  CreateDumpPath(m_DumpPath);
   general->Set("WirelessMac", m_WirelessMac);
-  general->Set("WiiSDCardPath", m_strWiiSDCardPath);
 
 #ifdef USE_GDBSTUB
 #ifndef _WIN32
@@ -430,13 +411,7 @@ void SConfig::LoadGeneralSettings(IniFile& ini)
   }
 
   general->Get("RecursiveISOPaths", &m_RecursiveISOFolder, false);
-  general->Get("NANDRootPath", &m_NANDPath);
-  File::SetUserPath(D_WIIROOT_IDX, m_NANDPath);
-  general->Get("DumpPath", &m_DumpPath);
-  CreateDumpPath(m_DumpPath);
   general->Get("WirelessMac", &m_WirelessMac);
-  general->Get("WiiSDCardPath", &m_strWiiSDCardPath, File::GetUserPath(F_WIISDCARD_IDX));
-  File::SetUserPath(F_WIISDCARD_IDX, m_strWiiSDCardPath);
 }
 
 void SConfig::LoadInterfaceSettings(IniFile& ini)
@@ -799,7 +774,6 @@ void SConfig::LoadDefaults()
   iBBDumpPort = -1;
   bSyncGPU = false;
   bFastDiscSpeed = false;
-  m_strWiiSDCardPath = File::GetUserPath(F_WIISDCARD_IDX);
   bEnableMemcardSdWriting = true;
   SelectedLanguage = 0;
   bOverrideGCLanguage = false;
diff --git a/Source/Core/Core/ConfigManager.h b/Source/Core/Core/ConfigManager.h
index 55e1e89466..f82598aa6e 100644
--- a/Source/Core/Core/ConfigManager.h
+++ b/Source/Core/Core/ConfigManager.h
@@ -185,7 +185,6 @@ struct SConfig
   std::string m_strBootROM;
   std::string m_strSRAM;
   std::string m_strDefaultISO;
-  std::string m_strWiiSDCardPath;
 
   std::string m_perfDir;
 
@@ -219,9 +218,6 @@ struct SConfig
   static IniFile LoadLocalGameIni(const std::string& id, std::optional<u16> revision);
   static IniFile LoadGameIni(const std::string& id, std::optional<u16> revision);
 
-  std::string m_NANDPath;
-  std::string m_DumpPath;
-
   std::string m_strMemoryCardA;
   std::string m_strMemoryCardB;
   std::string m_strGbaCartA;
diff --git a/Source/Core/DolphinQt2/Settings/PathPane.cpp b/Source/Core/DolphinQt2/Settings/PathPane.cpp
index 1f5b734368..eb379611a4 100644
--- a/Source/Core/DolphinQt2/Settings/PathPane.cpp
+++ b/Source/Core/DolphinQt2/Settings/PathPane.cpp
@@ -12,7 +12,8 @@
 #include <QPushButton>
 #include <QVBoxLayout>
 
-#include "Common/FileUtil.h"
+#include "Common/Config/Config.h"
+#include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
 
 #include "DolphinQt2/Settings.h"
@@ -55,7 +56,7 @@ void PathPane::BrowseDefaultGame()
 void PathPane::BrowseWiiNAND()
 {
   QString dir = QDir::toNativeSeparators(QFileDialog::getExistingDirectory(
-      this, tr("Select Wii NAND Root"), QString::fromStdString(SConfig::GetInstance().m_NANDPath)));
+      this, tr("Select Wii NAND Root"), QString::fromStdString(Config::Get(Config::MAIN_FS_PATH))));
   if (!dir.isEmpty())
   {
     m_nand_edit->setText(dir);
@@ -65,21 +66,19 @@ void PathPane::BrowseWiiNAND()
 
 void PathPane::BrowseDump()
 {
-  auto& dump_path = SConfig::GetInstance().m_DumpPath;
   QString dir = QDir::toNativeSeparators(QFileDialog::getExistingDirectory(
-      this, tr("Select Dump Path"), QString::fromStdString(dump_path)));
+      this, tr("Select Dump Path"), QString::fromStdString(Config::Get(Config::MAIN_DUMP_PATH))));
   if (!dir.isEmpty())
   {
     m_dump_edit->setText(dir);
-    dump_path = dir.toStdString();
+    Config::SetBase(Config::MAIN_DUMP_PATH, dir.toStdString());
   }
 }
 
 void PathPane::BrowseSDCard()
 {
   QString file = QDir::toNativeSeparators(QFileDialog::getOpenFileName(
-      this, tr("Select a SD Card Image"),
-      QString::fromStdString(SConfig::GetInstance().m_strWiiSDCardPath),
+      this, tr("Select a SD Card Image"), QString::fromStdString(Config::Get(Config::MAIN_SD_PATH)),
       tr("SD Card Image (*.raw);;"
          "All Files (*)")));
   if (!file.isEmpty())
@@ -91,18 +90,12 @@ void PathPane::BrowseSDCard()
 
 void PathPane::OnSDCardPathChanged()
 {
-  const auto sd_card_path = m_sdcard_edit->text().toStdString();
-
-  SConfig::GetInstance().m_strWiiSDCardPath = sd_card_path;
-  File::SetUserPath(F_WIISDCARD_IDX, sd_card_path);
+  Config::SetBase(Config::MAIN_SD_PATH, m_sdcard_edit->text().toStdString());
 }
 
 void PathPane::OnNANDPathChanged()
 {
-  const auto nand_path = m_nand_edit->text().toStdString();
-
-  SConfig::GetInstance().m_NANDPath = nand_path;
-  File::SetUserPath(D_WIIROOT_IDX, nand_path);
+  Config::SetBase(Config::MAIN_FS_PATH, m_nand_edit->text().toStdString());
 }
 
 QGroupBox* PathPane::MakeGameFolderBox()
@@ -170,7 +163,7 @@ QGridLayout* PathPane::MakePathsLayout()
   layout->addWidget(m_game_edit, 0, 1);
   layout->addWidget(game_open, 0, 2);
 
-  m_nand_edit = new QLineEdit(QString::fromStdString(SConfig::GetInstance().m_NANDPath));
+  m_nand_edit = new QLineEdit(QString::fromStdString(Config::Get(Config::MAIN_FS_PATH)));
   connect(m_nand_edit, &QLineEdit::editingFinished, this, &PathPane::OnNANDPathChanged);
   QPushButton* nand_open = new QPushButton(QStringLiteral("..."));
   connect(nand_open, &QPushButton::pressed, this, &PathPane::BrowseWiiNAND);
@@ -178,16 +171,16 @@ QGridLayout* PathPane::MakePathsLayout()
   layout->addWidget(m_nand_edit, 1, 1);
   layout->addWidget(nand_open, 1, 2);
 
-  m_dump_edit = new QLineEdit(QString::fromStdString(SConfig::GetInstance().m_DumpPath));
+  m_dump_edit = new QLineEdit(QString::fromStdString(Config::Get(Config::MAIN_DUMP_PATH)));
   connect(m_dump_edit, &QLineEdit::editingFinished,
-          [=] { SConfig::GetInstance().m_DumpPath = m_dump_edit->text().toStdString(); });
+          [=] { Config::SetBase(Config::MAIN_DUMP_PATH, m_dump_edit->text().toStdString()); });
   QPushButton* dump_open = new QPushButton(QStringLiteral("..."));
   connect(dump_open, &QPushButton::pressed, this, &PathPane::BrowseDump);
   layout->addWidget(new QLabel(tr("Dump Path:")), 2, 0);
   layout->addWidget(m_dump_edit, 2, 1);
   layout->addWidget(dump_open, 2, 2);
 
-  m_sdcard_edit = new QLineEdit(QString::fromStdString(SConfig::GetInstance().m_strWiiSDCardPath));
+  m_sdcard_edit = new QLineEdit(QString::fromStdString(Config::Get(Config::MAIN_SD_PATH)));
   connect(m_sdcard_edit, &QLineEdit::editingFinished, this, &PathPane::OnSDCardPathChanged);
   QPushButton* sdcard_open = new QPushButton(QStringLiteral("..."));
   connect(sdcard_open, &QPushButton::pressed, this, &PathPane::BrowseSDCard);
diff --git a/Source/Core/DolphinWX/Config/PathConfigPane.cpp b/Source/Core/DolphinWX/Config/PathConfigPane.cpp
index ce1c2a78a4..e06eeb4963 100644
--- a/Source/Core/DolphinWX/Config/PathConfigPane.cpp
+++ b/Source/Core/DolphinWX/Config/PathConfigPane.cpp
@@ -15,7 +15,8 @@
 #include <wx/sizer.h>
 #include <wx/stattext.h>
 
-#include "Common/FileUtil.h"
+#include "Common/Config/Config.h"
+#include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "DolphinWX/Config/ConfigMain.h"
@@ -101,9 +102,9 @@ void PathConfigPane::LoadGUIValues()
 
   m_recursive_iso_paths_checkbox->SetValue(SConfig::GetInstance().m_RecursiveISOFolder);
   m_default_iso_filepicker->SetPath(StrToWxStr(startup_params.m_strDefaultISO));
-  m_nand_root_dirpicker->SetPath(StrToWxStr(SConfig::GetInstance().m_NANDPath));
-  m_dump_path_dirpicker->SetPath(StrToWxStr(SConfig::GetInstance().m_DumpPath));
-  m_wii_sdcard_filepicker->SetPath(StrToWxStr(SConfig::GetInstance().m_strWiiSDCardPath));
+  m_nand_root_dirpicker->SetPath(StrToWxStr(Config::Get(Config::MAIN_FS_PATH)));
+  m_dump_path_dirpicker->SetPath(StrToWxStr(Config::Get(Config::MAIN_DUMP_PATH)));
+  m_wii_sdcard_filepicker->SetPath(StrToWxStr(Config::Get(Config::MAIN_SD_PATH)));
 
   // Update selected ISO paths
   for (const std::string& folder : SConfig::GetInstance().m_ISOFolder)
@@ -188,18 +189,12 @@ void PathConfigPane::OnDefaultISOChanged(wxCommandEvent& event)
 
 void PathConfigPane::OnSdCardPathChanged(wxCommandEvent& event)
 {
-  std::string sd_card_path = WxStrToStr(m_wii_sdcard_filepicker->GetPath());
-  SConfig::GetInstance().m_strWiiSDCardPath = sd_card_path;
-  File::SetUserPath(F_WIISDCARD_IDX, sd_card_path);
+  Config::SetBase(Config::MAIN_SD_PATH, WxStrToStr(m_wii_sdcard_filepicker->GetPath()));
 }
 
 void PathConfigPane::OnNANDRootChanged(wxCommandEvent& event)
 {
-  std::string nand_path = SConfig::GetInstance().m_NANDPath =
-      WxStrToStr(m_nand_root_dirpicker->GetPath());
-
-  File::SetUserPath(D_WIIROOT_IDX, nand_path);
-  m_nand_root_dirpicker->SetPath(StrToWxStr(nand_path));
+  Config::SetBase(Config::MAIN_FS_PATH, WxStrToStr(m_nand_root_dirpicker->GetPath()));
 
   wxCommandEvent update_event{DOLPHIN_EVT_UPDATE_LOAD_WII_MENU_ITEM, GetId()};
   update_event.SetEventObject(this);
@@ -208,10 +203,7 @@ void PathConfigPane::OnNANDRootChanged(wxCommandEvent& event)
 
 void PathConfigPane::OnDumpPathChanged(wxCommandEvent& event)
 {
-  std::string dump_path = SConfig::GetInstance().m_DumpPath =
-      WxStrToStr(m_dump_path_dirpicker->GetPath());
-
-  m_dump_path_dirpicker->SetPath(StrToWxStr(dump_path));
+  Config::SetBase(Config::MAIN_DUMP_PATH, WxStrToStr(m_dump_path_dirpicker->GetPath()));
 }
 
 void PathConfigPane::SaveISOPathChanges()
diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
index b4d3a8acfc..16fd08bad0 100644
--- a/Source/Core/UICommon/UICommon.cpp
+++ b/Source/Core/UICommon/UICommon.cpp
@@ -22,6 +22,7 @@
 #include "Common/MsgHandler.h"
 #include "Common/StringUtil.h"
 
+#include "Core/Config/MainSettings.h"
 #include "Core/ConfigLoaders/BaseConfigLoader.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
@@ -47,9 +48,31 @@
 
 namespace UICommon
 {
+static void CreateDumpPath(const std::string& path)
+{
+  if (path.empty())
+    return;
+  File::SetUserPath(D_DUMP_IDX, path + '/');
+  File::CreateFullPath(File::GetUserPath(D_DUMPAUDIO_IDX));
+  File::CreateFullPath(File::GetUserPath(D_DUMPDSP_IDX));
+  File::CreateFullPath(File::GetUserPath(D_DUMPSSL_IDX));
+  File::CreateFullPath(File::GetUserPath(D_DUMPFRAMES_IDX));
+  File::CreateFullPath(File::GetUserPath(D_DUMPTEXTURES_IDX));
+}
+
+static void InitCustomPaths()
+{
+  File::SetUserPath(D_WIIROOT_IDX, Config::Get(Config::MAIN_FS_PATH));
+  CreateDumpPath(Config::Get(Config::MAIN_DUMP_PATH));
+  const std::string sd_path = Config::Get(Config::MAIN_SD_PATH);
+  if (!sd_path.empty())
+    File::SetUserPath(F_WIISDCARD_IDX, sd_path);
+}
+
 void Init()
 {
   Config::Init();
+  Config::AddConfigChangedCallback(InitCustomPaths);
   Config::AddLayer(ConfigLoaders::GenerateBaseConfigLoader());
   SConfig::Init();
   LogManager::Init();