A system virtualizes applications on a managed endpoint using containers. A managed endpoint receives a virtualized container from an IT automation appliance. The virtualized container includes an application and a virtualization module. The virtualization module includes computer program instructions for virtualizing the application. An operating system API call made by the application during execution is intercepted, and a portion of the computer program instructions are executed based on the operating system API call. The computer program instructions modify the behavior of the application to effect the file and data virtualization of the application. A virtualized container can be deployed and updated from an IT automation appliance along with an agent to support the deployment and updating of the virtualized container.