The present subject mater relates to configuration of software applications and, more particularly, delta layering of software application content. The various embodiments described herein provide systems, methods, and software to store a first application instance in a first layer and modify the first application instance, wherein the modifying includes a modification to one or more items of first application instance content. Some embodiments further store the first application instance modifications in a second layer, wherein the second layer can be deployed to a second application instance.