diff --git a/es-app/src/main.cpp b/es-app/src/main.cpp
index c26cf6d5d..fcb4f218b 100644
--- a/es-app/src/main.cpp
+++ b/es-app/src/main.cpp
@@ -656,6 +656,8 @@ int main(int argc, char* argv[])
     Settings::getInstance()->setInt("ScreenHeight", 720);
 #endif
 
+    bool migratedSettings {false};
+
     {
         if (!Settings::getInstance()->getBool("LegacyAppDataDirectory")) {
             // Create the settings folder in the application data directory.
@@ -668,11 +670,33 @@ int main(int argc, char* argv[])
                     LOG(LogError) << "Couldn't create directory, permission problems?";
                 }
             }
+            std::filesystem::path settingsPathOld;
+            std::filesystem::path settingsPathNew;
+            settingsPathOld = Utils::FileSystem::getAppDataDirectory().append("es_settings.xml");
+            settingsPathNew = Utils::FileSystem::getAppDataDirectory()
+                                  .append("settings")
+                                  .append("es_settings.xml");
+            if (!Utils::FileSystem::existsSTD(settingsPathNew) &&
+                Utils::FileSystem::existsSTD(settingsPathOld)) {
+                Utils::FileSystem::renameFile(settingsPathOld.string(), settingsPathNew.string(),
+                                              false);
+                Settings::getInstance()->loadFile();
+                migratedSettings = true;
+            }
+            settingsPathOld = Utils::FileSystem::getAppDataDirectory().append("es_input.xml");
+            settingsPathNew =
+                Utils::FileSystem::getAppDataDirectory().append("settings").append("es_input.xml");
+            if (!Utils::FileSystem::existsSTD(settingsPathNew) &&
+                Utils::FileSystem::existsSTD(settingsPathOld)) {
+                Utils::FileSystem::renameFile(settingsPathOld.string(), settingsPathNew.string(),
+                                              false);
+                migratedSettings = true;
+            }
         }
     }
 
     {
-        // Check if the configuration file exists, and if not, create it.
+        // Check if the es_settings.xml file exists, and if not, create it.
         std::filesystem::path settingsPath;
         if (Settings::getInstance()->getBool("LegacyAppDataDirectory"))
             settingsPath = Utils::FileSystem::getAppDataDirectory().append("es_settings.xml");
@@ -788,6 +812,17 @@ int main(int argc, char* argv[])
                     LOG(LogWarning) << "Couldn't create directory, permission problems?";
                 }
             }
+            std::filesystem::path configPathOld {
+                Utils::FileSystem::getAppDataDirectory().append("es_controller_mappings.cfg")};
+            std::filesystem::path configPathNew {Utils::FileSystem::getAppDataDirectory()
+                                                     .append("controllers")
+                                                     .append("es_controller_mappings.cfg")};
+            if (!Utils::FileSystem::existsSTD(configPathNew) &&
+                Utils::FileSystem::existsSTD(configPathOld)) {
+                Utils::FileSystem::renameFile(configPathOld.string(), configPathNew.string(),
+                                              false);
+                migratedSettings = true;
+            }
         }
     }
 
@@ -951,6 +986,14 @@ int main(int argc, char* argv[])
         }
 #endif
 
+        if (Settings::getInstance()->getBool("LegacyAppDataDirectory"))
+            ViewController::getInstance()->legacyAppDataDialog();
+
+        if (migratedSettings) {
+            LOG(LogInfo) << "Migrated settings from a legacy application data directory structure";
+            ViewController::getInstance()->migratedAppDataFilesDialog();
+        }
+
         LOG(LogInfo) << "Application startup time: "
                      << std::chrono::duration_cast<std::chrono::milliseconds>(
                             std::chrono::system_clock::now() - applicationStartTime)
diff --git a/es-app/src/views/ViewController.cpp b/es-app/src/views/ViewController.cpp
index 0ef0208b0..65fe0766a 100644
--- a/es-app/src/views/ViewController.cpp
+++ b/es-app/src/views/ViewController.cpp
@@ -137,6 +137,41 @@ void ViewController::setMenuColors()
     }
 }
 
+void ViewController::legacyAppDataDialog()
+{
+    const std::string upgradeMessage {
+        "IN ES-DE 3.0 THE APPLICATION DATA DIRECTORY HAS CHANGED FROM \".emulationstation\" to "
+        "\"ES-DE\"\nPLEASE RENAME YOUR CURRENT DATA DIRECTORY:\n" +
+        Utils::FileSystem::getAppDataDirectory().string() + "\nTO THE FOLLOWING:\n" +
+        Utils::FileSystem::getAppDataDirectory().parent_path().append("ES-DE").string()};
+
+    mWindow->pushGui(new GuiMsgBox(
+        HelpStyle(), upgradeMessage.c_str(), "OK", [] {}, "", nullptr, "", nullptr, nullptr, true,
+        true,
+        (mRenderer->getIsVerticalOrientation() ?
+             0.85f :
+             0.55f * (1.778f / mRenderer->getScreenAspectRatio()))));
+}
+
+void ViewController::migratedAppDataFilesDialog()
+{
+    const std::string message {"SETTINGS HAVE BEEN MIGRATED FROM A LEGACY APPLICATION DATA "
+                               "DIRECTORY STRUCTURE, YOU NEED TO RESTART ES-DE TO APPLY "
+                               "THE CONFIGURATION"};
+
+    mWindow->pushGui(new GuiMsgBox(
+        HelpStyle(), message.c_str(), "QUIT",
+        [] {
+            SDL_Event quit;
+            quit.type = SDL_QUIT;
+            SDL_PushEvent(&quit);
+        },
+        "", nullptr, "", nullptr, nullptr, true, true,
+        (mRenderer->getIsVerticalOrientation() ?
+             0.65f :
+             0.55f * (1.778f / mRenderer->getScreenAspectRatio()))));
+}
+
 void ViewController::unsafeUpgradeDialog()
 {
     const std::string upgradeMessage {
@@ -146,6 +181,7 @@ void ViewController::unsafeUpgradeDialog()
         "MAKE SURE TO ALWAYS FOLLOW THE UPGRADE INSTRUCTIONS IN THE "
         "README.TXT FILE THAT CAN BE FOUND IN THE EMULATIONSTATION-DE "
         "DIRECTORY."};
+
     mWindow->pushGui(new GuiMsgBox(
         HelpStyle(), upgradeMessage.c_str(), "OK", [] {}, "", nullptr, "", nullptr, nullptr, true,
         true,
diff --git a/es-app/src/views/ViewController.h b/es-app/src/views/ViewController.h
index 125ae9ad6..18e65adf7 100644
--- a/es-app/src/views/ViewController.h
+++ b/es-app/src/views/ViewController.h
@@ -34,6 +34,8 @@ public:
 
     // These functions are called from main().
     void setMenuColors();
+    void legacyAppDataDialog();
+    void migratedAppDataFilesDialog();
     void unsafeUpgradeDialog();
     void invalidSystemsFileDialog();
     void noGamesDialog();