A deployment system enables a developer to customize a deployment plan generated according to a logical, multi-tier application blueprint for deploying multiple applications in a cloud infrastructure. Using the deployment system, the developer inserts a custom script or task in a sequence of tasks to be performed to deploy an application component in different phases (e.g., installation, configuration, start-up) on a virtual machine. The deployment system anchors the custom script to the different phases of the application component's deployment such that the customizations to the deployment plan are maintained through changes to the underlying application blueprint.