A service provider system may include an application fulfillment platform that delivers desktop applications on demand to desktops on physical computing devices or virtual desktop instances of end users. An application delivery agent installed on an end user's computing resource instance may store application state data (e.g., configuration data, runtime settings, or application templates) or scratch data that is generated by an application executing on the computing resource instance to a secure location on service provider storage resources. After a machine failure or change, or a rebuilding of a virtualized computing resource instance or virtual desktop instance, an application delivery agent installed on the new machine or instance may reinstall the application, retrieve the stored application state or scratch data from service provider resources, and restore the application to the last known persisted state. Upon request, the application delivery agent may restore the application to any earlier persisted state.