diff --git a/src/app/app.cpp b/src/app/app.cpp
index 87a93fb5a..db964981d 100644
--- a/src/app/app.cpp
+++ b/src/app/app.cpp
@@ -450,6 +450,14 @@ App::~App()
 
     delete m_legacy;
     delete m_modules;
+
+    // Save preferences only if we are running in GUI mode.  when we
+    // run in batch mode we might want to reset some preferences so
+    // the scripts have a reproducible behavior. Those reset
+    // preferences must not be saved.
+    if (isGui())
+      m_coreModules->m_preferences.save();
+
     delete m_coreModules;
 
 #ifdef ENABLE_UI
@@ -639,18 +647,14 @@ void app_rebuild_documents_tabs()
 
 PixelFormat app_get_current_pixel_format()
 {
-#ifdef ENABLE_UI
-  Context* context = UIContext::instance();
-  ASSERT(context != NULL);
+  Context* ctx = App::instance()->context();
+  ASSERT(ctx);
 
-  Doc* document = context->activeDocument();
-  if (document != NULL)
-    return document->sprite()->pixelFormat();
+  Doc* doc = ctx->activeDocument();
+  if (doc)
+    return doc->sprite()->pixelFormat();
   else
     return IMAGE_RGB;
-#else // ENABLE_UI
-  return IMAGE_RGB;
-#endif
 }
 
 void app_default_statusbar_message()
diff --git a/src/app/ini_file.cpp b/src/app/ini_file.cpp
index 3acacefa5..ed78e8dfd 100644
--- a/src/app/ini_file.cpp
+++ b/src/app/ini_file.cpp
@@ -1,5 +1,5 @@
 // Aseprite
-// Copyright (C) 2018  Igara Studio S.A.
+// Copyright (C) 2018-2019  Igara Studio S.A.
 // Copyright (C) 2001-2016  David Capello
 //
 // This program is distributed under the terms of
@@ -274,6 +274,11 @@ void del_config_value(const char* section, const char* name)
   g_configs.back()->deleteValue(section, name);
 }
 
+void del_config_section(const char* section)
+{
+  g_configs.back()->deleteSection(section);
+}
+
 base::paths enum_config_keys(const char* section)
 {
   base::paths keys;
diff --git a/src/app/ini_file.h b/src/app/ini_file.h
index 8c595cea2..db879e123 100644
--- a/src/app/ini_file.h
+++ b/src/app/ini_file.h
@@ -1,5 +1,5 @@
 // Aseprite
-// Copyright (C) 2018  Igara Studio S.A.
+// Copyright (C) 2018-2019  Igara Studio S.A.
 // Copyright (C) 2001-2016  David Capello
 //
 // This program is distributed under the terms of
@@ -58,6 +58,7 @@ namespace app {
   void set_config_color(const char* section, const char* name, const app::Color& value);
 
   void del_config_value(const char* section, const char* name);
+  void del_config_section(const char* section);
 
   base::paths enum_config_keys(const char* section);
 
diff --git a/src/app/pref/preferences.cpp b/src/app/pref/preferences.cpp
index 2c9b1d9d7..965fdb60b 100644
--- a/src/app/pref/preferences.cpp
+++ b/src/app/pref/preferences.cpp
@@ -1,5 +1,5 @@
 // Aseprite
-// Copyright (C) 2018  Igara Studio S.A.
+// Copyright (C) 2018-2019  Igara Studio S.A.
 // Copyright (C) 2001-2018  David Capello
 //
 // This program is distributed under the terms of
@@ -57,7 +57,9 @@ Preferences::Preferences()
 
 Preferences::~Preferences()
 {
-  save();
+  // Don't save preferences, this must be done by the client of the
+  // Preferences instance (the App class).
+  //save();
 
   for (auto& pair : m_tools)
     delete pair.second;
@@ -148,6 +150,16 @@ DocumentPreferences& Preferences::document(const Doc* doc)
   }
 }
 
+void Preferences::resetToolPreferences(tools::Tool* tool)
+{
+  auto it = m_tools.find(tool->getId());
+  if (it != m_tools.end())
+    m_tools.erase(it);
+
+  std::string section = std::string("tool.") + tool->getId();
+  del_config_section(section.c_str());
+}
+
 void Preferences::removeDocument(Doc* doc)
 {
   ASSERT(doc);
diff --git a/src/app/pref/preferences.h b/src/app/pref/preferences.h
index f9b0a8d54..b432ff45e 100644
--- a/src/app/pref/preferences.h
+++ b/src/app/pref/preferences.h
@@ -1,5 +1,5 @@
 // Aseprite
-// Copyright (C) 2018  Igara Studio S.A.
+// Copyright (C) 2018-2019  Igara Studio S.A.
 // Copyright (C) 2001-2018  David Capello
 //
 // This program is distributed under the terms of
@@ -64,6 +64,11 @@ namespace app {
     ToolPreferences& tool(tools::Tool* tool);
     DocumentPreferences& document(const Doc* doc);
 
+    // Used to reset the tool preferences in scripting mode when the
+    // UI is not available (so scripts have a common default
+    // preferences and a reproducible behavior for automation).
+    void resetToolPreferences(tools::Tool* tool);
+
     // Remove one document explicitly (this can be used if the
     // document used in Preferences::document() function wasn't member
     // of UIContext.
diff --git a/src/app/ui/editor/tool_loop_impl.cpp b/src/app/ui/editor/tool_loop_impl.cpp
index 6ce0908cd..cb8169b2f 100644
--- a/src/app/ui/editor/tool_loop_impl.cpp
+++ b/src/app/ui/editor/tool_loop_impl.cpp
@@ -337,7 +337,6 @@ public:
 #endif
   }
 
-
 };
 
 //////////////////////////////////////////////////////////////////////
@@ -534,6 +533,8 @@ public:
 #ifdef ENABLE_UI
     if (redraw)
       update_screen_for_document(m_document);
+#else
+    (void)redraw;               // To avoid warning about unused variable
 #endif
   }
 
@@ -700,6 +701,12 @@ tools::ToolLoop* create_tool_loop_for_script(
     const tools::ToolLoop::Button toolLoopButton = tools::ToolLoop::Left;
     tools::Controller* controller = tool->getController(toolLoopButton);
 
+    // If we don't have the UI available, we reset the tools
+    // preferences, so scripts that are executed in batch mode have a
+    // reproducible behavior.
+    if (!context->isUIAvailable())
+      Preferences::instance().resetToolPreferences(tool);
+
     return new ToolLoopImpl(
       nullptr, site, context,
       tool, ink, controller, brush,
diff --git a/src/cfg/LICENSE.txt b/src/cfg/LICENSE.txt
index aea0f6e8f..7585bab69 100644
--- a/src/cfg/LICENSE.txt
+++ b/src/cfg/LICENSE.txt
@@ -1,4 +1,5 @@
-Copyright (c) 2014 David Capello
+Copyright (C) 2019  Igara Studio S.A.
+Copyright (C) 2014-2017  David Capello
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
diff --git a/src/cfg/README.md b/src/cfg/README.md
index 8a1d9c014..02a0876c1 100644
--- a/src/cfg/README.md
+++ b/src/cfg/README.md
@@ -1,4 +1,3 @@
 # Aseprite Config Library
-*Copyright (C) 2014 David Capello*
 
 > Distributed under [MIT license](LICENSE.txt)
diff --git a/src/cfg/cfg.cpp b/src/cfg/cfg.cpp
index f8cd2aef6..c8fe17288 100644
--- a/src/cfg/cfg.cpp
+++ b/src/cfg/cfg.cpp
@@ -1,5 +1,6 @@
 // Aseprite Config Library
-// Copyright (c) 2014-2017 David Capello
+// Copyright (C) 2019  Igara Studio S.A.
+// Copyright (C) 2014-2017  David Capello
 //
 // This file is released under the terms of the MIT license.
 // Read LICENSE.txt for more information.
@@ -83,6 +84,10 @@ public:
     m_ini.Delete(section, name, true);
   }
 
+  void deleteSection(const char* section) {
+    m_ini.Delete(section, nullptr, true);
+  }
+
   void load(const std::string& filename) {
     m_filename = filename;
 
@@ -181,6 +186,11 @@ void CfgFile::deleteValue(const char* section, const char* name)
   m_impl->deleteValue(section, name);
 }
 
+void CfgFile::deleteSection(const char* section)
+{
+  m_impl->deleteSection(section);
+}
+
 void CfgFile::load(const std::string& filename)
 {
   m_impl->load(filename);
diff --git a/src/cfg/cfg.h b/src/cfg/cfg.h
index be5cd8d80..fef98afd0 100644
--- a/src/cfg/cfg.h
+++ b/src/cfg/cfg.h
@@ -1,5 +1,6 @@
 // Aseprite Config Library
-// Copyright (c) 2014-2016 David Capello
+// Copyright (C) 2019  Igara Studio S.A.
+// Copyright (C) 2014-2016  David Capello
 //
 // This file is released under the terms of the MIT license.
 // Read LICENSE.txt for more information.
@@ -34,6 +35,7 @@ namespace cfg {
     void setDoubleValue(const char* section, const char* name, double value);
 
     void deleteValue(const char* section, const char* name);
+    void deleteSection(const char* section);
 
     void load(const std::string& filename);
     void save();