diff --git a/src/async_handler.cpp b/src/async_handler.cpp
index 097416f6dd..744ceab6fc 100644
--- a/src/async_handler.cpp
+++ b/src/async_handler.cpp
@@ -243,6 +243,12 @@ FileRequestAsync* AsyncHandler::RequestFile(std::string_view file_name) {
 	return RequestFile(".", file_name);
 }
 
+FileRequestAsync* AsyncHandler::RequestFile(std::string_view preferred_dir, std::string_view fallback_dir, std::string_view file_name) {
+	auto* request = RequestFile(preferred_dir, file_name);
+	request->SetFallbackDirectory(fallback_dir);
+	return request;
+}
+
 bool AsyncHandler::IsFilePending(bool important, bool graphic) {
 	for (auto& ap: async_requests) {
 		FileRequestAsync& request = ap.second;
@@ -439,6 +445,20 @@ void FileRequestAsync::DownloadDone(bool success) {
 		success = state == State_DoneSuccess;
 	}
 
+	if (!success && !fallback_directory.empty()) {
+		// Not found in the current directory. On platforms without
+		// synchronous file access (Emscripten) this is the only way to
+		// learn that, since the file isn't present locally until it has
+		// actually been downloaded. Retry once in the fallback directory
+		// before giving up.
+		directory = std::move(fallback_directory);
+		fallback_directory.clear();
+		path = FileFinder::MakePath(directory, file);
+		state = State_WaitForStart;
+		Start();
+		return;
+	}
+
 	if (success) {
 #ifdef __EMSCRIPTEN__
 		if (state == State_Pending) {
diff --git a/src/async_handler.h b/src/async_handler.h
index e96aa9a50c..0b3dd5da13 100644
--- a/src/async_handler.h
+++ b/src/async_handler.h
@@ -69,6 +69,25 @@ namespace AsyncHandler {
 	 */
 	FileRequestAsync* RequestFile(std::string_view file_name);
 
+	/**
+	 * Creates a request to a file that may reside in one of two possible
+	 * directories, e.g. because a project can store it in a preferred
+	 * subfolder or (for compatibility) in the project root.
+	 * The file is requested from preferred_dir first. On platforms with
+	 * synchronous file access (i.e. everywhere except Emscripten) whether
+	 * the file actually exists there is already known at this point.
+	 * On platforms without synchronous access, existence can only be
+	 * determined by attempting the download: if that attempt fails, a
+	 * fallback request for fallback_dir is issued automatically, and the
+	 * request is only considered finished once that also completes.
+	 *
+	 * @param preferred_dir directory to try first
+	 * @param fallback_dir directory to fall back to when the file isn't in preferred_dir
+	 * @param file_name Name of the requested file requested.
+	 * @return The async request.
+	 */
+	FileRequestAsync* RequestFile(std::string_view preferred_dir, std::string_view fallback_dir, std::string_view file_name);
+
 	/**
 	 * Checks if any file with important-flag hasn't finished downloading yet.
 	 *
@@ -159,6 +178,17 @@ class FileRequestAsync {
 	 */
 	void SetGraphicFile(bool graphic);
 
+	/**
+	 * Sets a fallback directory to retry the request in when it fails in
+	 * its current directory (see AsyncHandler::RequestFile with a
+	 * preferred/fallback directory pair). Only one fallback attempt is
+	 * made.
+	 * This must be set before Start() is invoked.
+	 *
+	 * @param dir directory to retry the request in on failure.
+	 */
+	void SetFallbackDirectory(std::string_view dir);
+
 	/**
 	 * Starts the async requests.
 	 * When the request was already started earlier and is pending this call
@@ -218,6 +248,7 @@ class FileRequestAsync {
 	std::string directory;
 	std::string file;
 	std::string path;
+	std::string fallback_directory;
 	int state = State_DoneFailure;
 	bool important = false;
 	bool graphic = false;
@@ -255,6 +286,10 @@ inline void FileRequestAsync::SetImportantFile(bool important) {
 	this->important = important;
 }
 
+inline void FileRequestAsync::SetFallbackDirectory(std::string_view dir) {
+	fallback_directory = ToString(dir);
+}
+
 inline bool FileRequestAsync::IsGraphicFile() const {
 	return graphic;
 }
diff --git a/src/fileext_guesser.cpp b/src/fileext_guesser.cpp
index 568e891960..558ed89dd6 100644
--- a/src/fileext_guesser.cpp
+++ b/src/fileext_guesser.cpp
@@ -67,17 +67,10 @@ FileExtGuesser::RPG2KNonStandardFilenameGuesser FileExtGuesser::GetRPG2kProjectW
 	return RPG2KNonStandardFilenameGuesser();
 }
 
-void FileExtGuesser::GuessAndAddLmuExtension(const FilesystemView& fs, Meta const& meta, RPG2KFileExtRemap& mapping)
-{
-	// If metadata is provided, rely on that.
-	std::string metaLmu = meta.GetLmuAlias();
-	if (!metaLmu.empty()) {
-		mapping.extMap[SUFFIX_LMU] = metaLmu;
-		Output::Debug("Metadata-provided non-standard extension for LMU({})", metaLmu);
-	} else {
-		// Try to rescue and determine file extensions.
-		// Without metadata, scan for matching files. Stop after you find a few;
-		//   we can't just pick the first since there may be some backup files on disk.
+namespace {
+	// Scans a single directory for "mapXXXX.???" files and guesses the LMU
+	// extension from whichever non-standard extension occurs most often.
+	void GuessLmuExtensionIn(const FilesystemView& fs, FileExtGuesser::RPG2KFileExtRemap& mapping) {
 		std::unordered_map<std::string, int> extCounts; // ext => count
 
 		const auto* entries = fs.ListDirectory();
@@ -94,7 +87,7 @@ void FileExtGuesser::GuessAndAddLmuExtension(const FilesystemView& fs, Meta cons
 					if (extCounts[ext] >= 5) {
 						mapping.extMap[SUFFIX_LMU] = ext;
 						Output::Debug("Guessing non-standard extension for LMU({})", ext);
-						break;
+						return;
 					}
 				}
 			}
@@ -102,6 +95,30 @@ void FileExtGuesser::GuessAndAddLmuExtension(const FilesystemView& fs, Meta cons
 	}
 }
 
+void FileExtGuesser::GuessAndAddLmuExtension(const FilesystemView& fs, Meta const& meta, RPG2KFileExtRemap& mapping)
+{
+	// If metadata is provided, rely on that.
+	std::string metaLmu = meta.GetLmuAlias();
+	if (!metaLmu.empty()) {
+		mapping.extMap[SUFFIX_LMU] = metaLmu;
+		Output::Debug("Metadata-provided non-standard extension for LMU({})", metaLmu);
+		return;
+	}
+
+	// Try to rescue and determine file extensions.
+	// Without metadata, scan for matching files. Stop after you find a few;
+	//   we can't just pick the first since there may be some backup files on disk.
+	// Maps are preferably stored in the "Map" subfolder, but fall back to
+	// the project root for games that keep their maps there.
+	FilesystemView maps_fs = fs.Subtree(MAP_DIR_NAME);
+	if (maps_fs) {
+		GuessLmuExtensionIn(maps_fs, mapping);
+	}
+	if (mapping.extMap.find(SUFFIX_LMU) == mapping.extMap.end()) {
+		GuessLmuExtensionIn(fs, mapping);
+	}
+}
+
 FileExtGuesser::RPG2KFileExtRemap FileExtGuesser::RPG2KNonStandardFilenameGuesser::guessExtensions(Meta& meta)
 {
 	RPG2KFileExtRemap res;
diff --git a/src/game_map.cpp b/src/game_map.cpp
index b4acc5b50b..d8c253e803 100644
--- a/src/game_map.cpp
+++ b/src/game_map.cpp
@@ -330,11 +330,11 @@ std::unique_ptr<lcf::rpg::Map> Game_Map::LoadMapFile(int map_id) {
 	// FIXME: Assert map was cached for async platforms
 	bool map_is_easyrpg_file = Player::player_config.prefer_easyrpg_map_files.Get();
 	std::string map_name = Game_Map::ConstructMapName(map_id, map_is_easyrpg_file);
-	std::string map_file = FileFinder::Game().FindFile(map_name);
+	std::string map_file = Game_Map::FindMapFile(map_name);
 	if (map_file.empty()) {
 		map_is_easyrpg_file = !map_is_easyrpg_file;
 		map_name = Game_Map::ConstructMapName(map_id, map_is_easyrpg_file);
-		map_file = FileFinder::Game().FindFile(map_name);
+		map_file = Game_Map::FindMapFile(map_name);
 
 		if (map_file.empty()) {
 			Output::Error("Loading of Map {} failed.\nThe map was not found.", map_name);
@@ -2017,12 +2017,31 @@ std::string Game_Map::ConstructMapName(int map_id, bool is_easyrpg) {
 	}
 }
 
+std::string Game_Map::FindMapFile(std::string_view map_name) {
+	// Maps are preferably stored in the "Map" subfolder, but fall back to
+	// the game's root directory for compatibility with games that keep
+	// their maps there.
+	std::string map_file = FileFinder::Game().FindFile(MAP_DIR_NAME, map_name);
+	if (map_file.empty()) {
+		map_file = FileFinder::Game().FindFile(map_name);
+	}
+	return map_file;
+}
+
 FileRequestAsync* Game_Map::RequestMap(int map_id) {
 #ifdef __EMSCRIPTEN__
 	Player::translation.RequestAndAddMap(map_id);
 #endif
 
-	auto* request = AsyncHandler::RequestFile(Game_Map::ConstructMapName(map_id, false));
+	std::string map_name = Game_Map::ConstructMapName(map_id, false);
+
+	// On platforms with synchronous file access, FindMapFile() above could
+	// tell us upfront which directory the map is in. But on platforms like
+	// Emscripten a file isn't available locally until it has actually been
+	// downloaded, so existence can't be probed in advance: request the
+	// preferred directory and let AsyncHandler fall back to the root
+	// directory automatically if that attempt fails.
+	auto* request = AsyncHandler::RequestFile(MAP_DIR_NAME, ".", map_name);
 	request->SetImportantFile(true);
 	return request;
 }
diff --git a/src/game_map.h b/src/game_map.h
index 81384edeb3..c413ae141a 100644
--- a/src/game_map.h
+++ b/src/game_map.h
@@ -710,6 +710,16 @@ namespace Game_Map {
 	 */
 	std::string ConstructMapName(int map_id, bool is_easyrpg);
 
+	/**
+	 * Searches for a map file on disk. Maps are preferably stored in the
+	 * "Map" subfolder, but the game's root directory is also searched for
+	 * compatibility with existing games that were never reorganized.
+	 *
+	 * @param map_name The filename to search for, as returned by ConstructMapName
+	 * @return Path to the found file, or an empty string when not found
+	 */
+	std::string FindMapFile(std::string_view map_name);
+
 	FileRequestAsync* RequestMap(int map_id);
 
 	namespace Caching {
diff --git a/src/options.h b/src/options.h
index a20e88c994..4b1f7d941f 100644
--- a/src/options.h
+++ b/src/options.h
@@ -82,6 +82,10 @@
 #define TREEMAP_NAME RPG_RT_PREFIX "." SUFFIX_LMT
 #define TREEMAP_NAME_EASYRPG EASY_RT_PREFIX "." SUFFIX_EMT
 
+/** Subfolder that map files (.lmu/.emu) are preferably stored in.
+ *  Games that still keep them in the project root are also supported. */
+#define MAP_DIR_NAME "Map"
+
 /** File name for additional metadata, such as multi-game save imports. */
 #define META_NAME "Meta.ini"
 
diff --git a/src/player.cpp b/src/player.cpp
index 1ff38f8c6c..9aabcb8762 100644
--- a/src/player.cpp
+++ b/src/player.cpp
@@ -995,8 +995,8 @@ static bool DefaultLmuStartFileExists(const FilesystemView& fs) {
 	int map_id = Player::start_map_id == -1 ? lcf::Data::treemap.start.party_map_id : Player::start_map_id;
 	std::string mapName = Game_Map::ConstructMapName(map_id, false);
 
-	// Now see if the file exists.
-	return !fs.FindFile(mapName).empty();
+	// Now see if the file exists, preferring the "Map" subfolder.
+	return !fs.FindFile(MAP_DIR_NAME, mapName).empty() || !fs.FindFile(mapName).empty();
 }
 
 void Player::GuessNonStandardExtensions() {