User configurations of an installed application are migrated by isolating them from a base application state of the installed application to generate a virtual application package. At runtime, a base virtual application package and a user configurations virtual application package are provisioned from a central repository and executed by the user. The resulting virtualized execution environment merges the application resources contained in the packages such that the user configurations override the base application to make available all of the user configurations. This technique may be used to preserve user configurations during migration of applications, or to maintain user-specific configurations for a particular application across different sessions of a user's virtualized desktop.