An automated physical database backup, refresh and cloning system and method automatically generates scripts or commands for implementing one or more tasks related to physical database backup and/or database and application refresh or cloning operations between a source environment and a target environment. The scripts or commands make use of parameters describing the source and target environments, at least some of which are gathered prior to initiating backup and cloning. The tasks are performed during one or more backup, refresh and cloning phases. In some embodiments, scripts are automatically regenerated and executed after a failure associated with the source or target environment.