System and methods are described for implementing controlled updates of containers in a distributed application deployment environment. In one implementation, a method comprises: receiving a request to update a target container of a plurality of containers within a deployed computing unit; identifying an updated configuration object to be applied to the target container based on the request; receiving or computing a health indicator representative of performance of the deployed computing unit or other containers to which the updated configuration object has been applied; and assigning the updated configuration object to the target container based on the health indicator.