diff --git a/src/common/common_paths.h b/src/common/common_paths.h
index 0e2fe8a98..609fb44da 100644
--- a/src/common/common_paths.h
+++ b/src/common/common_paths.h
@@ -19,17 +19,22 @@
 #else
 #ifdef _WIN32
 #define EMU_DATA_DIR "Lime3DS"
+#define LEGACY_EMU_DATA_DIR "Citra"
 #elif defined(__APPLE__)
 #include <TargetConditionals.h>
-#if TARGET_OS_IPHONE
+#if TARGET_OS_IPHONE // TODO: Kill iOS
 #define APPLE_EMU_DATA_DIR "Documents" DIR_SEP "Lime3DS"
+#define LEGACY_APPLE_EMU_DATA_DIR "Documents" DIR_SEP "Citra"
 #else
 #define APPLE_EMU_DATA_DIR "Library" DIR_SEP "Application Support" DIR_SEP "Lime3DS"
+#define LEGACY_APPLE_EMU_DATA_DIR "Library" DIR_SEP "Application Support" DIR_SEP "Citra"
 #endif
 // For compatibility with XDG paths.
 #define EMU_DATA_DIR "lime3ds-emu"
+#define LEGACY_EMU_DATA_DIR "citra-emu"
 #else
 #define EMU_DATA_DIR "lime3ds-emu"
+#define LEGACY_EMU_DATA_DIR "citra-emu"
 #endif
 #endif
 
diff --git a/src/common/file_util.cpp b/src/common/file_util.cpp
index 3e052454f..08bafc37c 100644
--- a/src/common/file_util.cpp
+++ b/src/common/file_util.cpp
@@ -771,8 +771,11 @@ void SetUserPath(const std::string& path) {
     } else {
 #ifdef _WIN32
         user_path = GetExeDirectory() + DIR_SEP USERDATA_DIR DIR_SEP;
+        std::string& legacy_user_path = g_paths[UserPath::LegacyUserDir];
+
         if (!FileUtil::IsDirectory(user_path)) {
             user_path = AppDataRoamingDirectory() + DIR_SEP EMU_DATA_DIR DIR_SEP;
+            legacy_user_path = AppDataRoamingDirectory() + DIR_SEP LEGACY_EMU_DATA_DIR DIR_SEP;
         } else {
             LOG_INFO(Common_Filesystem, "Using the local user directory");
         }
@@ -784,6 +787,7 @@ void SetUserPath(const std::string& path) {
         g_paths.emplace(UserPath::ConfigDir, user_path + CONFIG_DIR DIR_SEP);
         g_paths.emplace(UserPath::CacheDir, user_path + CACHE_DIR DIR_SEP);
 #else
+        std::string& legacy_user_path = g_paths[UserPath::LegacyUserDir];
         auto current_dir = FileUtil::GetCurrentDir();
         if (current_dir.has_value() &&
             FileUtil::Exists(current_dir.value() + USERDATA_DIR DIR_SEP)) {
@@ -792,10 +796,16 @@ void SetUserPath(const std::string& path) {
             g_paths.emplace(UserPath::CacheDir, user_path + CACHE_DIR DIR_SEP);
         } else {
             std::string data_dir = GetUserDirectory("XDG_DATA_HOME") + DIR_SEP EMU_DATA_DIR DIR_SEP;
+            std::string legacy_data_dir =
+                GetUserDirectory("XDG_DATA_HOME") + DIR_SEP LEGACY_EMU_DATA_DIR DIR_SEP;
             std::string config_dir =
                 GetUserDirectory("XDG_CONFIG_HOME") + DIR_SEP EMU_DATA_DIR DIR_SEP;
             std::string cache_dir =
                 GetUserDirectory("XDG_CACHE_HOME") + DIR_SEP EMU_DATA_DIR DIR_SEP;
+            g_paths.emplace(UserPath::LegacyConfigDir, GetUserDirectory("XDG_CONFIG_HOME") +
+                                                           DIR_SEP LEGACY_EMU_DATA_DIR DIR_SEP);
+            g_paths.emplace(UserPath::LegacyCacheDir, GetUserDirectory("XDG_CACHE_HOME") +
+                                                          DIR_SEP LEGACY_EMU_DATA_DIR DIR_SEP);
 
 #if defined(__APPLE__)
             // If XDG directories don't already exist from a previous setup, use standard macOS
@@ -803,12 +813,14 @@ void SetUserPath(const std::string& path) {
             if (!FileUtil::Exists(data_dir) && !FileUtil::Exists(config_dir) &&
                 !FileUtil::Exists(cache_dir)) {
                 data_dir = GetHomeDirectory() + DIR_SEP APPLE_EMU_DATA_DIR DIR_SEP;
+                legacy_data_dir = GetHomeDirectory() + DIR_SEP LEGACY_APPLE_EMU_DATA_DIR DIR_SEP;
                 config_dir = data_dir + CONFIG_DIR DIR_SEP;
                 cache_dir = data_dir + CACHE_DIR DIR_SEP;
             }
 #endif
 
             user_path = data_dir;
+            legacy_user_path = legacy_data_dir;
             g_paths.emplace(UserPath::ConfigDir, config_dir);
             g_paths.emplace(UserPath::CacheDir, cache_dir);
         }
diff --git a/src/common/file_util.h b/src/common/file_util.h
index c24beeb7a..c0fa49d7d 100644
--- a/src/common/file_util.h
+++ b/src/common/file_util.h
@@ -32,17 +32,20 @@ enum class UserPath {
     ConfigDir,
     DLLDir,
     DumpDir,
+    IconsDir,
+    LegacyCacheDir,  // LegacyCacheDir and LegacyConfigDir are only defined if migrating these
+    LegacyConfigDir, // directories is necessary (aka not a child of LegacyUserDir)
+    LegacyUserDir,
     LoadDir,
     LogDir,
     NANDDir,
+    PlayTimeDir,
     RootDir,
     SDMCDir,
     ShaderDir,
     StatesDir,
     SysDataDir,
     UserDir,
-    IconsDir,
-    PlayTimeDir,
 };
 
 // Replaces install-specific paths with standard placeholders, and back again
diff --git a/src/lime_qt/main.cpp b/src/lime_qt/main.cpp
index 5023063a4..5d54c00e9 100644
--- a/src/lime_qt/main.cpp
+++ b/src/lime_qt/main.cpp
@@ -159,12 +159,16 @@ static QString PrettyProductName() {
 
 GMainWindow::GMainWindow(Core::System& system_)
     : ui{std::make_unique<Ui::MainWindow>()}, system{system_}, movie{system.Movie()},
-      config{std::make_unique<Config>()}, emu_thread{nullptr} {
+      emu_thread{nullptr} {
     Common::Log::Initialize();
     Common::Log::Start();
 
     Debugger::ToggleConsole();
 
+    CheckForMigration();
+
+    this->config = std::make_unique<Config>();
+
 #ifdef __unix__
     SetGamemodeEnabled(Settings::values.enable_gamemode.GetValue());
 #endif
@@ -1099,6 +1103,55 @@ void GMainWindow::ShowUpdaterWidgets() {
 }
 #endif
 
+void GMainWindow::CheckForMigration() {
+    namespace fs = std::filesystem;
+    if (fs::is_directory(FileUtil::GetUserPath(FileUtil::UserPath::LegacyUserDir)) &&
+        !fs::is_directory(FileUtil::GetUserPath(FileUtil::UserPath::UserDir))) {
+        if (QMessageBox::information(
+                this, tr("Migration"),
+                tr("Lime3DS has moved to a new data directory.\n\n"
+                   "Would you like to migrate your Citra data to this new "
+                   "location?\n"
+                   "(This may take a while; The old data will not be deleted)"),
+                QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes) == QMessageBox::Yes) {
+            MigrateUserData();
+        } else {
+            QMessageBox::information(this, tr("Migration"),
+                                     tr("You can manually re-trigger this prompt by deleting the "
+                                        "new user data directory:\n"
+                                        "%1")
+                                         .arg(QString::fromStdString(
+                                             FileUtil::GetUserPath(FileUtil::UserPath::UserDir))),
+                                     QMessageBox::Ok);
+        }
+    }
+}
+
+void GMainWindow::MigrateUserData() {
+    namespace fs = std::filesystem;
+    const auto copyOptions = fs::copy_options::update_existing | fs::copy_options::recursive;
+
+    fs::copy(FileUtil::GetUserPath(FileUtil::UserPath::LegacyUserDir),
+             FileUtil::GetUserPath(FileUtil::UserPath::UserDir), copyOptions);
+    if (fs::is_directory(FileUtil::GetUserPath(FileUtil::UserPath::LegacyConfigDir))) {
+        fs::copy(FileUtil::GetUserPath(FileUtil::UserPath::LegacyConfigDir),
+                 FileUtil::GetUserPath(FileUtil::UserPath::ConfigDir), copyOptions);
+    }
+    if (fs::is_directory(FileUtil::GetUserPath(FileUtil::UserPath::LegacyCacheDir))) {
+        fs::copy(FileUtil::GetUserPath(FileUtil::UserPath::LegacyCacheDir),
+                 FileUtil::GetUserPath(FileUtil::UserPath::CacheDir), copyOptions);
+    }
+
+    QMessageBox::information(
+        this, tr("Migration"),
+        tr("Data was migrated successfully. Lime3DS will now start.\n\n"
+           "If you wish to clean up the files which were left in the old data location, you can do "
+           "so by deleting the following directory:\n"
+           "%1")
+            .arg(QString::fromStdString(FileUtil::GetUserPath(FileUtil::UserPath::LegacyUserDir))),
+        QMessageBox::Ok);
+}
+
 #if defined(HAVE_SDL2) && defined(__unix__) && !defined(__APPLE__)
 static std::optional<QDBusObjectPath> HoldWakeLockLinux(u32 window_id = 0) {
     if (!QDBusConnection::sessionBus().isConnected()) {
diff --git a/src/lime_qt/main.h b/src/lime_qt/main.h
index 03e55013f..774668bfa 100644
--- a/src/lime_qt/main.h
+++ b/src/lime_qt/main.h
@@ -171,6 +171,9 @@ private:
     void CheckForUpdates();
 #endif
 
+    void CheckForMigration();
+    void MigrateUserData();
+
     /**
      * Stores the filename in the recently loaded files list.
      * The new filename is stored at the beginning of the recently loaded files list.