Systems and methods are described for bootstrapping an application with metadata specified in a template. The template specifies a stack of resources that will be used to execute an application and also includes a set of metadata for customizing the resources and the application. When the system receives the template, it instantiates a compute node which will execute the application. The compute node may contain at least one initialization script for bootstrapping the application with the metadata contained in the template. This functionality allows users to bootstrap the application running on the compute node with data from within the template that was used to create the stack of resources for executing the application. In this manner, metadata, configuration files, package names and versions can be passed by the application owner to the remote compute node.