Embodiments of the present invention address deficiencies of the art in respect to dependency maintenance when updating a base application and provide a method, system and computer program product for base and stack application dependency synchronization when updating the base application. In one embodiment of the invention, a method for base and stack application dependency synchronization can be provided for when updating the base application in a multi-application software system. The method can include separating an update to the multi-application software system into a core update for a base application in the multi-application software system and multiple different anchors, each anchor corresponding to at least one stack application. The method further can include installing the core update to the base application and only those of the anchors corresponding to those of the stack applications installed for the base application.