Methods and arrangements are described for controlling transitions between firing fractions during skip fire operation of an engine in order to help smooth the transitions. Generally, firing fractions transitions are implemented gradually, preferably in a manner that relatively closely tracks manifold filling dynamics. In some embodiments, the commanded firing fraction is altered each firing opportunity. Another approach contemplates altering the commanded firing fraction by substantially the same amount each firing opportunity for at least a portion of the transition. These approaches work particularly well when the commanded firing fraction is provided to a skip fire controller that includes an accumulator functionality that tracks the portion of a firing that has been requested, but not delivered, or vice versa. In various embodiments, commanded firing fraction changes are delayed relative to initiation of the change in throttle position to help compensate for inherent delays associated with changing the manifold air pressure.