Methods and controllers for coordinating firing fraction transitions that occur in conjunction with transmission shifts are described. In one aspect, an engine controller transmits a do-not-shift instruction to a transmission controller based at least in part on a determination that a particular type of firing fraction transition is desired. The firing fraction transition is then implemented using a skip fire transition protocol. In this manner, the transmission is affirmatively prevented from shifting during the firing fraction transition. The described approaches are well suited for use in connection with transitions to DCCO or DFCO operation.