diff --git a/cura/CuraApplication.py b/cura/CuraApplication.py
index 6321dbf670..c3477ed252 100755
--- a/cura/CuraApplication.py
+++ b/cura/CuraApplication.py
@@ -26,7 +26,6 @@ from UM.Settings.Validator import Validator
 from UM.Message import Message
 from UM.i18n import i18nCatalog
 from UM.Workspace.WorkspaceReader import WorkspaceReader
-from UM.Platform import Platform
 from UM.Decorators import deprecated
 
 from UM.Operations.AddSceneNodeOperation import AddSceneNodeOperation
@@ -268,6 +267,9 @@ class CuraApplication(QtApplication):
         with ContainerRegistry.getInstance().lockFile():
             ContainerRegistry.getInstance().load()
 
+        # set the setting version for Preferences
+        Preferences.getInstance().setSettingVersion(CuraApplication.SettingVersion)
+
         Preferences.getInstance().addPreference("cura/active_mode", "simple")
 
         Preferences.getInstance().addPreference("cura/categories_expanded", "")
diff --git a/plugins/VersionUpgrade/VersionUpgrade25to26/VersionUpgrade25to26.py b/plugins/VersionUpgrade/VersionUpgrade25to26/VersionUpgrade25to26.py
index d3e22ba5d2..7d728884cb 100644
--- a/plugins/VersionUpgrade/VersionUpgrade25to26/VersionUpgrade25to26.py
+++ b/plugins/VersionUpgrade/VersionUpgrade25to26/VersionUpgrade25to26.py
@@ -61,8 +61,13 @@ class VersionUpgrade25to26(VersionUpgrade):
             parser["general"]["visible_settings"] = ";".join(new_visible_settings)
 
         #Change the version number in the file.
+        if "general" not in parser:
+            parser["general"] = {}
         parser.set("general", "version", "4")
-        parser.set("general", "setting_version", "1")
+
+        if "metadata" not in parser:
+            parser["metadata"] = {}
+        parser.set("metadata", "setting_version", "1")
 
         #Re-serialise the file.
         output = io.StringIO()
diff --git a/plugins/VersionUpgrade/VersionUpgrade26to27/VersionUpgrade26to27.py b/plugins/VersionUpgrade/VersionUpgrade26to27/VersionUpgrade26to27.py
index 38031765d5..e2d7817077 100644
--- a/plugins/VersionUpgrade/VersionUpgrade26to27/VersionUpgrade26to27.py
+++ b/plugins/VersionUpgrade/VersionUpgrade26to27/VersionUpgrade26to27.py
@@ -87,6 +87,50 @@ class VersionUpgrade26to27(VersionUpgrade):
         setting_version = int(parser.get("metadata", "setting_version", fallback = 0))
         return format_version * 1000000 + setting_version
 
+    ##  Upgrades a preferences file from version 2.6 to 2.7.
+    #
+    #   \param serialised The serialised form of a preferences file.
+    #   \param filename The name of the file to upgrade.
+    def upgradePreferences(self, serialised, filename):
+        parser = configparser.ConfigParser(interpolation=None)
+        parser.read_string(serialised)
+
+        # Update version numbers
+        if "general" not in parser:
+            parser["general"] = {}
+        parser["general"]["version"] = "4"
+
+        if "metadata" not in parser:
+            parser["metadata"] = {}
+        parser["metadata"]["setting_version"] = "2"
+
+        # Re-serialise the file.
+        output = io.StringIO()
+        parser.write(output)
+        return [filename], [output.getvalue()]
+
+    ##  Upgrades a container file other than a container stack file from version 2.6 to 2.7.
+    #
+    #   \param serialised The serialised form of a container file.
+    #   \param filename The name of the file to upgrade.
+    def upgradeOtherContainer(self, serialised, filename):
+        parser = configparser.ConfigParser(interpolation=None)
+        parser.read_string(serialised)
+
+        # Update version numbers
+        if "general" not in parser:
+            parser["general"] = {}
+        parser["general"]["version"] = "2"
+
+        if "metadata" not in parser:
+            parser["metadata"] = {}
+        parser["metadata"]["setting_version"] = "2"
+
+        # Re-serialise the file.
+        output = io.StringIO()
+        parser.write(output)
+        return [filename], [output.getvalue()]
+
     ##  Upgrades a container stack from version 2.6 to 2.7.
     #
     #   \param serialised The serialised form of a container stack.
@@ -108,12 +152,15 @@ class VersionUpgrade26to27(VersionUpgrade):
             if not parser.has_section(each_section):
                 parser.add_section(each_section)
 
-        # Change the version number in the file.
-        parser["metadata"]["setting_version"] = str(CuraApplication.SettingVersion)
-
-        # Update version
+        # Update version numbers
+        if "general" not in parser:
+            parser["general"] = {}
         parser["general"]["version"] = "3"
 
+        if "metadata" not in parser:
+            parser["metadata"] = {}
+        parser["metadata"]["setting_version"] = "2"
+
         # Re-serialise the file.
         output = io.StringIO()
         parser.write(output)
diff --git a/plugins/VersionUpgrade/VersionUpgrade26to27/__init__.py b/plugins/VersionUpgrade/VersionUpgrade26to27/__init__.py
index 8ddf4aa7ea..b0c0d70ae2 100644
--- a/plugins/VersionUpgrade/VersionUpgrade26to27/__init__.py
+++ b/plugins/VersionUpgrade/VersionUpgrade26to27/__init__.py
@@ -14,6 +14,21 @@ def getMetaData():
             # From                          To                             Upgrade function
             ("machine_stack", 3000000):     ("machine_stack", 3000002,     upgrade.upgradeStack),
             ("extruder_train", 3000000):    ("extruder_train", 3000002,    upgrade.upgradeStack),
+
+            # In 2.6.x, Preferences are saved with "version = 4" and no setting_version.
+            # This means those Preferences files will still be treated as "4.0" as defined in VersionUpgrade25to26,
+            # so the 25to26 upgrade routine will be called again.
+            #
+            # To fix this, we first fix the upgrade routine for 25to26 so it actually upgrades to "4.1", and then
+            # here we can upgrade from "4.1" to "4.2" safely.
+            #
+            ("preferences", 4000001):       ("preferences", 4000002,         upgrade.upgradePreferences),
+            # NOTE: All the instance containers share the same general/version, so we have to update all of them
+            #       if any is updated.
+            ("quality_changes", 2000001):       ("quality_changes", 2000002,    upgrade.upgradeOtherContainer),
+            ("user", 2000001):                  ("user", 2000002,               upgrade.upgradeOtherContainer),
+            ("quality", 2000001):               ("quality", 2000002,            upgrade.upgradeOtherContainer),
+            ("definition_changes", 2000001):    ("definition_changes", 2000002, upgrade.upgradeOtherContainer),
         },
         "sources": {
             "machine_stack": {
@@ -24,6 +39,22 @@ def getMetaData():
                 "get_version": upgrade.getCfgVersion,
                 "location": {"./extruders"}
             },
+            "preferences": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"."}
+            },
+            "quality_changes": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"./quality"}
+            },
+            "user": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"./user"}
+            },
+            "definition_changes": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"./machine_instances"}
+            }
         }
     }