diff --git a/src/app/commands/cmd_options.cpp b/src/app/commands/cmd_options.cpp
index 80f0ce451..4ce87bd19 100644
--- a/src/app/commands/cmd_options.cpp
+++ b/src/app/commands/cmd_options.cpp
@@ -182,7 +182,8 @@ class OptionsWindow : public app::gen::Options {
     void uninstall() {
       ASSERT(m_extension);
       ASSERT(canBeUninstalled());
-      App::instance()->extensions().uninstallExtension(m_extension);
+      App::instance()->extensions().uninstallExtension(m_extension,
+                                                       DeletePluginPref::kYes);
       m_extension = nullptr;
     }
 
@@ -1445,7 +1446,7 @@ private:
 
         // Uninstall old version
         if (ext->canBeUninstalled()) {
-          exts.uninstallExtension(ext);
+          exts.uninstallExtension(ext, DeletePluginPref::kNo);
 
           ExtensionItem* item = getItemByExtension(ext);
           if (item)
diff --git a/src/app/extensions.cpp b/src/app/extensions.cpp
index e97febdcd..5874c4287 100644
--- a/src/app/extensions.cpp
+++ b/src/app/extensions.cpp
@@ -1,5 +1,5 @@
 // Aseprite
-// Copyright (C) 2020  Igara Studio S.A.
+// Copyright (C) 2020-2022  Igara Studio S.A.
 // Copyright (C) 2017-2018  David Capello
 //
 // This program is distributed under the terms of
@@ -353,7 +353,7 @@ void Extension::enable(const bool state)
 #endif // ENABLE_SCRIPTING
 }
 
-void Extension::uninstall()
+void Extension::uninstall(const DeletePluginPref delPref)
 {
   if (!m_isInstalled)
     return;
@@ -366,14 +366,15 @@ void Extension::uninstall()
         m_name.c_str(), m_path.c_str());
 
   // Remove all files inside the extension path
-  uninstallFiles(m_path);
-  ASSERT(!base::is_directory(m_path));
+  uninstallFiles(m_path, delPref);
+  ASSERT(!base::is_directory(m_path) || delPref == DeletePluginPref::kNo);
 
   m_isEnabled = false;
   m_isInstalled = false;
 }
 
-void Extension::uninstallFiles(const std::string& path)
+void Extension::uninstallFiles(const std::string& path,
+                               const DeletePluginPref delPref)
 {
 #if 1 // Read the list of files to be uninstalled from __info.json file
 
@@ -398,11 +399,17 @@ void Extension::uninstallFiles(const std::string& path)
     }
   }
 
-  // Delete __pref.lua file
+  // Delete __pref.lua file (only if specified, e.g. if the user is
+  // updating the extension, the preferences should be kept).
+  bool hasPrefFile = false;
   {
     std::string fn = base::join_path(path, kPrefLua);
-    if (base::is_file(fn))
-      base::delete_file(fn);
+    if (base::is_file(fn)) {
+      if (delPref == DeletePluginPref::kYes)
+        base::delete_file(fn);
+      else
+        hasPrefFile = true;
+    }
   }
 
   std::sort(installedDirs.begin(),
@@ -427,7 +434,8 @@ void Extension::uninstallFiles(const std::string& path)
   }
 
   TRACE("EXT: Deleting extension directory '%s'\n", path.c_str());
-  base::remove_directory(path);
+  if (!hasPrefFile)
+    base::remove_directory(path);
 
 #else // The following code delete the whole "path",
       // we prefer the __info.json approach.
@@ -439,7 +447,7 @@ void Extension::uninstallFiles(const std::string& path)
       base::delete_file(fn);
     }
     else if (base::is_directory(fn)) {
-      uninstallFiles(fn);
+      uninstallFiles(fn, deleteUserPref);
     }
   }
 
@@ -860,9 +868,10 @@ void Extensions::enableExtension(Extension* extension, const bool state)
   generateExtensionSignals(extension);
 }
 
-void Extensions::uninstallExtension(Extension* extension)
+void Extensions::uninstallExtension(Extension* extension,
+                                    const DeletePluginPref delPref)
 {
-  extension->uninstall();
+  extension->uninstall(delPref);
   generateExtensionSignals(extension);
 
   auto it = std::find(m_extensions.begin(),
diff --git a/src/app/extensions.h b/src/app/extensions.h
index 00b222d27..3561b0c6f 100644
--- a/src/app/extensions.h
+++ b/src/app/extensions.h
@@ -31,6 +31,8 @@ namespace app {
     std::string commonPath;
   };
 
+  enum DeletePluginPref { kNo, kYes };
+
   class Extension {
     friend class Extensions;
   public:
@@ -113,8 +115,9 @@ namespace app {
 
   private:
     void enable(const bool state);
-    void uninstall();
-    void uninstallFiles(const std::string& path);
+    void uninstall(const DeletePluginPref delPref);
+    void uninstallFiles(const std::string& path,
+                        const DeletePluginPref delPref);
     bool isCurrentTheme() const;
     bool isDefaultTheme() const;
     void updateCategory(const Category newCategory);
@@ -172,7 +175,8 @@ namespace app {
     iterator end() { return m_extensions.end(); }
 
     void enableExtension(Extension* extension, const bool state);
-    void uninstallExtension(Extension* extension);
+    void uninstallExtension(Extension* extension,
+                            const DeletePluginPref delPref);
     ExtensionInfo getCompressedExtensionInfo(const std::string& zipFn);
     Extension* installCompressedExtension(const std::string& zipFn,
                                           const ExtensionInfo& info);