diff --git a/es-app/src/FileData.cpp b/es-app/src/FileData.cpp
index c753ca383..5cc5f393a 100644
--- a/es-app/src/FileData.cpp
+++ b/es-app/src/FileData.cpp
@@ -431,12 +431,30 @@ void FileData::sort(ComparisonFunction& comparator, bool ascending,
     mOnlyFolders = true;
     mHasFolders = false;
     bool foldersOnTop = Settings::getInstance()->getBool("FoldersOnTop");
+    bool showHiddenGames = Settings::getInstance()->getBool("ShowHiddenGames");
     std::vector<FileData*> mChildrenFolders;
     std::vector<FileData*> mChildrenOthers;
 
     if (mSystem->isGroupedCustomCollection())
         gameCount = {};
 
+    if (!showHiddenGames) {
+        for (auto it = mChildren.begin(); it != mChildren.end();) {
+        // If the option to hide hidden games has been set and the game is hidden,
+        // then skip it. Normally games are hidden during loading of the gamelists in
+        // Gamelist::parseGamelist() and this code should only run when a user has marked
+        // an entry manually as hidden. So upon the next application startup, this game
+        // should be filtered already at that earlier point.
+            if ((*it)->getHidden())
+                it = mChildren.erase(it);
+            // Also hide folders where all its entries have been hidden.
+            else if ((*it)->getType() == FOLDER && (*it)->getChildren().size() == 0)
+                it = mChildren.erase(it);
+            else
+                it++;
+        }
+    }
+
     // The main custom collections view is sorted during startup in CollectionSystemManager.
     // The individual collections are however sorted as any normal systems/folders.
     if (mSystem->isCollection() && mSystem->getFullName() == "collections") {
@@ -524,11 +542,12 @@ void FileData::sortFavoritesOnTop(ComparisonFunction& comparator, bool ascending
 {
     mOnlyFolders = true;
     mHasFolders = false;
+    bool foldersOnTop = Settings::getInstance()->getBool("FoldersOnTop");
+    bool showHiddenGames = Settings::getInstance()->getBool("ShowHiddenGames");
     std::vector<FileData*> mChildrenFolders;
     std::vector<FileData*> mChildrenFavoritesFolders;
     std::vector<FileData*> mChildrenFavorites;
     std::vector<FileData*> mChildrenOthers;
-    bool foldersOnTop = Settings::getInstance()->getBool("FoldersOnTop");
 
     if (mSystem->isGroupedCustomCollection())
         gameCount = {};
@@ -549,6 +568,17 @@ void FileData::sortFavoritesOnTop(ComparisonFunction& comparator, bool ascending
     }
 
     for (unsigned int i = 0; i < mChildren.size(); i++) {
+        // If the option to hide hidden games has been set and the game is hidden,
+        // then skip it. Normally games are hidden during loading of the gamelists in
+        // Gamelist::parseGamelist() and this code should only run when a user has marked
+        // an entry manually as hidden. So upon the next application startup, this game
+        // should be filtered already at that earlier point.
+        if (!showHiddenGames && mChildren[i]->getHidden())
+            continue;
+        // Also hide folders where all its entries have been hidden.
+        else if (mChildren[i]->getType() == FOLDER && mChildren[i]->getChildren().size() == 0)
+            continue;
+
         // Game count, which will be displayed in the system view.
         if (mChildren[i]->getType() == GAME && mChildren[i]->getCountAsGame()) {
             if (!mChildren[i]->getFavorite())
diff --git a/es-app/src/Gamelist.cpp b/es-app/src/Gamelist.cpp
index 6311b23a1..6afc43655 100644
--- a/es-app/src/Gamelist.cpp
+++ b/es-app/src/Gamelist.cpp
@@ -164,11 +164,17 @@ void parseGamelist(SystemData* system)
             // games, then delete the entry. This leaves no trace of the entry at all in ES
             // but that is fine as the option to show hidden files is defined as requiring an
             // application restart.
-            if (!Settings::getInstance()->getBool("ShowHiddenGames") && file->getHidden()) {
-                LOG(LogDebug) << "Gamelist::parseGamelist(): Skipping hidden " <<
-                        (type == GAME ? "file" : "folder") << " entry \"" <<
-                        file->getName() << "\"" << " (\"" << file->getPath() << "\")";
-                delete file;
+            if (!Settings::getInstance()->getBool("ShowHiddenGames")) {
+                if (file->getHidden()) {
+                    LOG(LogDebug) << "Gamelist::parseGamelist(): Skipping hidden " <<
+                            (type == GAME ? "file" : "folder") << " entry \"" <<
+                            file->getName() << "\"" << " (\"" << file->getPath() << "\")";
+                    delete file;
+                }
+                // Also delete any folders which are empty, i.e. all their entries are hidden.
+                else if (file->getType() == FOLDER && file->getChildren().size() == 0) {
+                    delete file;
+                }
             }
         }
     }
diff --git a/es-app/src/guis/GuiMetaDataEd.cpp b/es-app/src/guis/GuiMetaDataEd.cpp
index 904ef786e..cad04fbd1 100644
--- a/es-app/src/guis/GuiMetaDataEd.cpp
+++ b/es-app/src/guis/GuiMetaDataEd.cpp
@@ -352,7 +352,7 @@ void GuiMetaDataEd::save()
         mMetaData->set(mMetaDataDecl.at(i).key, mEditors.at(i)->getValue());
     }
 
-    // If hidden games are not shown and the hide flag was set for the game, then write the
+    // If hidden games are not shown and the hide flag was set for the entry, then write the
     // metadata immediately regardless of the SaveGamelistsMode setting. Otherwise the file
     // will never be written as the game will be filtered from the gamelist. This solution is not
     // really good as the gamelist will be written twice, but it's a very special and hopefully
@@ -376,6 +376,12 @@ void GuiMetaDataEd::save()
 
     mScraperParams.system->onMetaDataSavePoint();
 
+    // If hidden games are not shown and the hide flag was set for the entry, we also need
+    // to re-sort the gamelist as we may need to remove the parent folder if all the entries
+    // within this folder are now hidden.
+    if (hideGameWhileHidden)
+        mScraperParams.system->sortSystem(true);
+
     // Make sure that the cached background is updated to reflect any possible visible
     // changes to the gamelist (e.g. the game name).
     mWindow->invalidateCachedBackground();