Various methods and data structures for managing transition between different firing fractions during skip fire operation of an engine are described. In some embodiments, transitions are constrained to occur when firing sequence segments of a designated length are shared by the first and second firing fractions. In a separate aspect, a data structure that uses current firing fraction phase as a first index and a target firing fraction as a second index may be used to determine a phase of the target firing fraction to enter at a transition. Is some circumstances transitions between a current and target firing fraction may be conducted as a series of steps through intermediate firing fractions.