A variety of methods and arrangements are described for controlling transitions between firing fractions during skip fire and potentially variable displacement operation of an engine. In general, cam first transition strategies are described in which the cam phase is changed to, or close to a target cam phase before a corresponding firing fraction change is implemented. When the cam phase change associated with a desired firing fraction change is relatively large, the firing fraction change is divided into a series of two or more firing fraction change steps—with each step using a cam first transition approach. A number of intermediate target selection schemes are described as well.