diff --git a/launcher/minecraft/mod/ModFolderModel.cpp b/launcher/minecraft/mod/ModFolderModel.cpp
index 112d219ec..d4c5e8191 100644
--- a/launcher/minecraft/mod/ModFolderModel.cpp
+++ b/launcher/minecraft/mod/ModFolderModel.cpp
@@ -63,6 +63,9 @@ void ModFolderModel::startWatching()
     if(is_watching)
         return;
 
+    // Remove orphaned metadata next time
+    m_first_folder_load = true;
+
     update();
 
     // Watch the mods folder
@@ -113,7 +116,8 @@ bool ModFolderModel::update()
     }
 
     auto index_dir = indexDir();
-    auto task = new ModFolderLoadTask(dir(), index_dir, m_is_indexed);
+    auto task = new ModFolderLoadTask(dir(), index_dir, m_is_indexed, m_first_folder_load);
+    m_first_folder_load = false;
 
     m_update = task->result();
 
diff --git a/launcher/minecraft/mod/ModFolderModel.h b/launcher/minecraft/mod/ModFolderModel.h
index a7d3ece04..3d6efac31 100644
--- a/launcher/minecraft/mod/ModFolderModel.h
+++ b/launcher/minecraft/mod/ModFolderModel.h
@@ -172,6 +172,7 @@ protected:
     bool interaction_disabled = false;
     QDir m_dir;
     bool m_is_indexed;
+    bool m_first_folder_load = true;
     QMap<QString, int> modsIndex;
     QMap<int, LocalModParseTask::ResultPtr> activeTickets;
     int nextResolutionTicket = 0;
diff --git a/launcher/minecraft/mod/tasks/ModFolderLoadTask.cpp b/launcher/minecraft/mod/tasks/ModFolderLoadTask.cpp
index 9b70e7a1a..015ead80e 100644
--- a/launcher/minecraft/mod/tasks/ModFolderLoadTask.cpp
+++ b/launcher/minecraft/mod/tasks/ModFolderLoadTask.cpp
@@ -38,8 +38,8 @@
 
 #include "minecraft/mod/MetadataHandler.h"
 
-ModFolderLoadTask::ModFolderLoadTask(QDir& mods_dir, QDir& index_dir, bool is_indexed) 
-    : m_mods_dir(mods_dir), m_index_dir(index_dir), m_is_indexed(is_indexed), m_result(new Result())
+ModFolderLoadTask::ModFolderLoadTask(QDir& mods_dir, QDir& index_dir, bool is_indexed, bool clean_orphan)
+    : m_mods_dir(mods_dir), m_index_dir(index_dir), m_is_indexed(is_indexed), m_clean_orphan(clean_orphan), m_result(new Result())
 {}
 
 void ModFolderLoadTask::run()
@@ -85,12 +85,14 @@ void ModFolderLoadTask::run()
 
     // Remove orphan metadata to prevent issues
     // See https://github.com/PolyMC/PolyMC/issues/996
-    QMutableMapIterator<QString, Mod::Ptr> iter(m_result->mods);
-    while (iter.hasNext()) {
-        auto mod = iter.next().value();
-        if (mod->status() == ModStatus::NotInstalled) {
-            mod->destroy(m_index_dir, false);
-            iter.remove();
+    if (m_clean_orphan) {
+        QMutableMapIterator<QString, Mod::Ptr> iter(m_result->mods);
+        while (iter.hasNext()) {
+            auto mod = iter.next().value();
+            if (mod->status() == ModStatus::NotInstalled) {
+                mod->destroy(m_index_dir, false);
+                iter.remove();
+            }
         }
     }
 
diff --git a/launcher/minecraft/mod/tasks/ModFolderLoadTask.h b/launcher/minecraft/mod/tasks/ModFolderLoadTask.h
index 0b6bb6cc2..1f2015d2b 100644
--- a/launcher/minecraft/mod/tasks/ModFolderLoadTask.h
+++ b/launcher/minecraft/mod/tasks/ModFolderLoadTask.h
@@ -56,7 +56,7 @@ public:
     }
 
 public:
-    ModFolderLoadTask(QDir& mods_dir, QDir& index_dir, bool is_indexed);
+    ModFolderLoadTask(QDir& mods_dir, QDir& index_dir, bool is_indexed, bool clean_orphan = false);
     void run();
 signals:
     void succeeded();
@@ -67,5 +67,6 @@ private:
 private:
     QDir& m_mods_dir, m_index_dir;
     bool m_is_indexed;
+    bool m_clean_orphan;
     ResultPtr m_result;
 };