diff --git a/Source/Core/Core/WiiUtils.cpp b/Source/Core/Core/WiiUtils.cpp
index 4ce3f03103..f721107d76 100644
--- a/Source/Core/Core/WiiUtils.cpp
+++ b/Source/Core/Core/WiiUtils.cpp
@@ -685,4 +685,89 @@ UpdateResult DoDiscUpdate(UpdateCallback update_callback, const std::string& ima
   DiscIO::NANDContentManager::Access().ClearCache();
   return result;
 }
+
+bool CheckNAND(IOS::HLE::Kernel& ios)
+{
+  bool bad = false;
+  const auto es = ios.GetES();
+
+  // Check for NANDs that were used with old Dolphin versions.
+  if (File::Exists(Common::RootUserPath(Common::FROM_CONFIGURED_ROOT) + "/sys/replace"))
+  {
+    ERROR_LOG(CORE, "CheckNAND: NAND was used with old versions, so it is likely to be damaged");
+    bad = true;
+  }
+
+  for (const u64 title_id : es->GetInstalledTitles())
+  {
+    // Check for missing title sub directories.
+    if (!File::IsDirectory(Common::GetTitleContentPath(title_id, Common::FROM_CONFIGURED_ROOT)))
+    {
+      ERROR_LOG(CORE, "CheckNAND: Missing content directory for title %016" PRIx64, title_id);
+      bad = true;
+    }
+    if (!File::IsDirectory(Common::GetTitleDataPath(title_id, Common::FROM_CONFIGURED_ROOT)))
+    {
+      ERROR_LOG(CORE, "CheckNAND: Missing data directory for title %016" PRIx64, title_id);
+      bad = true;
+    }
+
+    // Check for incomplete title installs (missing ticket, TMD or contents).
+    const auto ticket = DiscIO::FindSignedTicket(title_id);
+    if (!IOS::ES::IsDiscTitle(title_id) && !ticket.IsValid())
+    {
+      ERROR_LOG(CORE, "CheckNAND: Missing ticket for title %016" PRIx64, title_id);
+      bad = true;
+    }
+
+    const auto tmd = es->FindInstalledTMD(title_id);
+    if (!tmd.IsValid())
+    {
+      WARN_LOG(CORE, "CheckNAND: Missing TMD for title %016" PRIx64, title_id);
+      // Further checks require the TMD to be valid.
+      continue;
+    }
+
+    const auto installed_contents = es->GetStoredContentsFromTMD(tmd);
+    const bool is_installed = std::any_of(installed_contents.begin(), installed_contents.end(),
+                                          [](const auto& content) { return !content.IsShared(); });
+
+    if (is_installed && installed_contents != tmd.GetContents() &&
+        (tmd.GetTitleFlags() & IOS::ES::TitleFlags::TITLE_TYPE_WFS_MAYBE) == 0)
+    {
+      ERROR_LOG(CORE, "CheckNAND: Missing contents for title %016" PRIx64, title_id);
+      bad = true;
+    }
+  }
+
+  return !bad;
+}
+
+bool RepairNAND(IOS::HLE::Kernel& ios)
+{
+  const auto es = ios.GetES();
+
+  // Delete an old, unneeded file
+  File::Delete(Common::RootUserPath(Common::FROM_CONFIGURED_ROOT) + "/sys/replace");
+
+  for (const u64 title_id : es->GetInstalledTitles())
+  {
+    // Create missing title sub directories.
+    const std::string content_dir =
+        Common::GetTitleContentPath(title_id, Common::FROM_CONFIGURED_ROOT);
+    const std::string data_dir = Common::GetTitleDataPath(title_id, Common::FROM_CONFIGURED_ROOT);
+    File::CreateDir(content_dir);
+    File::CreateDir(data_dir);
+
+    // If there's nothing in the content/data directories and no ticket,
+    // this title shouldn't exist at all on the NAND.
+    if (File::ScanDirectoryTree(content_dir, false).children.empty() &&
+        File::ScanDirectoryTree(data_dir, false).children.empty() &&
+        !DiscIO::FindSignedTicket(title_id).IsValid())
+    {
+      es->DeleteTitle(title_id);
+    }
+  }
+  return CheckNAND(ios);
+}
 }
diff --git a/Source/Core/Core/WiiUtils.h b/Source/Core/Core/WiiUtils.h
index 49e8175bc2..2320b1f154 100644
--- a/Source/Core/Core/WiiUtils.h
+++ b/Source/Core/Core/WiiUtils.h
@@ -12,6 +12,14 @@
 
 // Small utility functions for common Wii related tasks.
 
+namespace IOS
+{
+namespace HLE
+{
+class Kernel;
+}
+}
+
 namespace WiiUtils
 {
 bool InstallWAD(const std::string& wad_path);
@@ -48,4 +56,8 @@ UpdateResult DoOnlineUpdate(UpdateCallback update_callback, const std::string& r
 
 // Perform a disc update with behaviour similar to the System Menu.
 UpdateResult DoDiscUpdate(UpdateCallback update_callback, const std::string& image_path);
+
+// Check the emulated NAND for common issues.
+bool CheckNAND(IOS::HLE::Kernel& ios);
+bool RepairNAND(IOS::HLE::Kernel& ios);
 }
diff --git a/Source/Core/DolphinQt2/MenuBar.cpp b/Source/Core/DolphinQt2/MenuBar.cpp
index 6fb6cc79a5..b7b7410e6f 100644
--- a/Source/Core/DolphinQt2/MenuBar.cpp
+++ b/Source/Core/DolphinQt2/MenuBar.cpp
@@ -22,6 +22,7 @@
 #include "Core/IOS/IOS.h"
 #include "Core/Movie.h"
 #include "Core/State.h"
+#include "Core/WiiUtils.h"
 #include "DiscIO/NANDImporter.h"
 #include "DolphinQt2/AboutDialog.h"
 #include "DolphinQt2/GameList/GameFile.h"
@@ -114,7 +115,7 @@ void MenuBar::AddToolsMenu()
       AddAction(tools_menu, QStringLiteral(""), this, [this] { emit BootWiiSystemMenu(); });
   m_import_backup = AddAction(gc_ipl, tr("Import BootMii NAND Backup..."), this,
                               [this] { emit ImportNANDBackup(); });
-
+  m_check_nand = AddAction(tools_menu, tr("Check NAND..."), this, &MenuBar::CheckNAND);
   m_extract_certificates = AddAction(tools_menu, tr("Extract Certificates from NAND"), this,
                                      &MenuBar::NANDExtractCertificates);
 
@@ -473,6 +474,7 @@ void MenuBar::UpdateToolsMenu(bool emulation_started)
   m_pal_ipl->setEnabled(!emulation_started &&
                         File::Exists(SConfig::GetInstance().GetBootROMPath(EUR_DIR)));
   m_import_backup->setEnabled(!emulation_started);
+  m_check_nand->setEnabled(!emulation_started);
 
   if (!emulation_started)
   {
@@ -532,6 +534,35 @@ void MenuBar::ExportWiiSaves()
   CWiiSaveCrypted::ExportAllSaves();
 }
 
+void MenuBar::CheckNAND()
+{
+  IOS::HLE::Kernel ios;
+  if (WiiUtils::CheckNAND(ios))
+  {
+    QMessageBox::information(this, tr("NAND Check"), tr("No issues have been detected."));
+    return;
+  }
+
+  if (QMessageBox::question(
+          this, tr("NAND Check"),
+          tr("The emulated NAND is damaged. System titles such as the Wii Menu and "
+             "the Wii Shop Channel may not work correctly.\n\n"
+             "Do you want to try to repair the NAND?")) != QMessageBox::Yes)
+  {
+    return;
+  }
+
+  if (WiiUtils::RepairNAND(ios))
+  {
+    QMessageBox::information(this, tr("NAND Check"), tr("The NAND has been repaired."));
+    return;
+  }
+
+  QMessageBox::critical(this, tr("NAND Check"),
+                        tr("The NAND could not be repaired. It is recommended to back up "
+                           "your current data and start over with a fresh NAND."));
+}
+
 void MenuBar::NANDExtractCertificates()
 {
   if (DiscIO::NANDImporter().ExtractCertificates(File::GetUserPath(D_WIIROOT_IDX)))
diff --git a/Source/Core/DolphinQt2/MenuBar.h b/Source/Core/DolphinQt2/MenuBar.h
index c4a8c6a41c..d9745e7e67 100644
--- a/Source/Core/DolphinQt2/MenuBar.h
+++ b/Source/Core/DolphinQt2/MenuBar.h
@@ -113,6 +113,7 @@ private:
   void InstallWAD();
   void ImportWiiSave();
   void ExportWiiSaves();
+  void CheckNAND();
   void NANDExtractCertificates();
 
   void OnSelectionChanged(QSharedPointer<GameFile> game_file);
@@ -131,6 +132,7 @@ private:
   QAction* m_ntscu_ipl;
   QAction* m_pal_ipl;
   QAction* m_import_backup;
+  QAction* m_check_nand;
   QAction* m_extract_certificates;
 
   // Emulation
diff --git a/Source/Core/DolphinWX/Frame.h b/Source/Core/DolphinWX/Frame.h
index a7005841ef..24cb56a94b 100644
--- a/Source/Core/DolphinWX/Frame.h
+++ b/Source/Core/DolphinWX/Frame.h
@@ -348,6 +348,7 @@ private:
   void OnInstallWAD(wxCommandEvent& event);
   void OnUninstallWAD(wxCommandEvent& event);
   void OnImportBootMiiBackup(wxCommandEvent& event);
+  void OnCheckNAND(wxCommandEvent& event);
   void OnExtractCertificates(wxCommandEvent& event);
   void OnPerformOnlineWiiUpdate(wxCommandEvent& event);
   void OnPerformDiscWiiUpdate(wxCommandEvent& event);
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index e8c7b4f487..cda03e9c6d 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -185,6 +185,7 @@ void CFrame::BindMenuBarEvents()
   Bind(wxEVT_MENU, &CFrame::OnInstallWAD, this, IDM_MENU_INSTALL_WAD);
   Bind(wxEVT_MENU, &CFrame::OnLoadWiiMenu, this, IDM_LOAD_WII_MENU);
   Bind(wxEVT_MENU, &CFrame::OnImportBootMiiBackup, this, IDM_IMPORT_NAND);
+  Bind(wxEVT_MENU, &CFrame::OnCheckNAND, this, IDM_CHECK_NAND);
   Bind(wxEVT_MENU, &CFrame::OnExtractCertificates, this, IDM_EXTRACT_CERTIFICATES);
   for (const int idm : {IDM_PERFORM_ONLINE_UPDATE_CURRENT, IDM_PERFORM_ONLINE_UPDATE_EUR,
                         IDM_PERFORM_ONLINE_UPDATE_JPN, IDM_PERFORM_ONLINE_UPDATE_KOR,
@@ -1308,6 +1309,34 @@ void CFrame::OnImportBootMiiBackup(wxCommandEvent& WXUNUSED(event))
   UpdateLoadWiiMenuItem();
 }
 
+void CFrame::OnCheckNAND(wxCommandEvent&)
+{
+  IOS::HLE::Kernel ios;
+  if (WiiUtils::CheckNAND(ios))
+  {
+    wxMessageBox(_("No issues have been detected."), _("NAND Check"), wxOK | wxICON_INFORMATION);
+    return;
+  }
+
+  if (wxMessageBox("The emulated NAND is damaged. System titles such as the Wii Menu and "
+                   "the Wii Shop Channel may not work correctly.\n\n"
+                   "Do you want to try to repair the NAND?",
+                   _("NAND Check"), wxYES_NO) != wxYES)
+  {
+    return;
+  }
+
+  if (WiiUtils::RepairNAND(ios))
+  {
+    wxMessageBox(_("The NAND has been repaired."), _("NAND Check"), wxOK | wxICON_INFORMATION);
+    return;
+  }
+
+  wxMessageBox(_("The NAND could not be repaired. It is recommended to back up "
+                 "your current data and start over with a fresh NAND."),
+               _("NAND Check"), wxOK | wxICON_ERROR);
+}
+
 void CFrame::OnExtractCertificates(wxCommandEvent& WXUNUSED(event))
 {
   DiscIO::NANDImporter().ExtractCertificates(File::GetUserPath(D_WIIROOT_IDX));
diff --git a/Source/Core/DolphinWX/Globals.h b/Source/Core/DolphinWX/Globals.h
index dad9550cd7..1975716bce 100644
--- a/Source/Core/DolphinWX/Globals.h
+++ b/Source/Core/DolphinWX/Globals.h
@@ -105,6 +105,7 @@ enum
   IDM_LIST_INSTALL_WAD,
   IDM_LIST_UNINSTALL_WAD,
   IDM_IMPORT_NAND,
+  IDM_CHECK_NAND,
   IDM_EXTRACT_CERTIFICATES,
   IDM_PERFORM_ONLINE_UPDATE_CURRENT,
   IDM_PERFORM_ONLINE_UPDATE_EUR,
diff --git a/Source/Core/DolphinWX/MainMenuBar.cpp b/Source/Core/DolphinWX/MainMenuBar.cpp
index c9b505e891..fdb6b633c6 100644
--- a/Source/Core/DolphinWX/MainMenuBar.cpp
+++ b/Source/Core/DolphinWX/MainMenuBar.cpp
@@ -235,6 +235,7 @@ wxMenu* MainMenuBar::CreateToolsMenu() const
   tools_menu->Append(IDM_MENU_INSTALL_WAD, _("Install WAD..."));
   tools_menu->Append(IDM_LOAD_WII_MENU, dummy_string);
   tools_menu->Append(IDM_IMPORT_NAND, _("Import BootMii NAND Backup..."));
+  tools_menu->Append(IDM_CHECK_NAND, _("Check NAND..."));
   tools_menu->Append(IDM_EXTRACT_CERTIFICATES, _("Extract Certificates from NAND"));
   auto* const online_update_menu = new wxMenu;
   online_update_menu->Append(IDM_PERFORM_ONLINE_UPDATE_CURRENT, _("Current Region"));
@@ -582,7 +583,7 @@ void MainMenuBar::RefreshWiiToolsLabels() const
   // inconsistent data.
   const bool enable_wii_tools = !Core::IsRunning() || !SConfig::GetInstance().bWii;
   for (const int index :
-       {IDM_MENU_INSTALL_WAD, IDM_EXPORT_ALL_SAVE, IDM_IMPORT_SAVE, IDM_IMPORT_NAND,
+       {IDM_MENU_INSTALL_WAD, IDM_EXPORT_ALL_SAVE, IDM_IMPORT_SAVE, IDM_IMPORT_NAND, IDM_CHECK_NAND,
         IDM_EXTRACT_CERTIFICATES, IDM_LOAD_WII_MENU, IDM_PERFORM_ONLINE_UPDATE_CURRENT,
         IDM_PERFORM_ONLINE_UPDATE_EUR, IDM_PERFORM_ONLINE_UPDATE_JPN, IDM_PERFORM_ONLINE_UPDATE_KOR,
         IDM_PERFORM_ONLINE_UPDATE_USA})