An application power controller controls power supplied from rechargeable battery packs to a set of aircraft in-flight processing systems that are executing applications. Operations access a repository of application information to obtain a list of applications to be executed by the aircraft in-flight processing systems and power consumption information for the applications. Further operations obtain information from the battery monitor indicating health and capacity of the battery packs. The operations initiate an application deactivation action based on determining that the indicated health and/or capacity of the battery packs does not satisfy a battery protection rule defining constraints on battery usage. The operations then select one of the applications from among the list that is to be deactivated responsive to the application deactivation action, and communicate a command to at least one of the in-flight application processing systems to trigger the selected application to cease being executed.