A variety of skip fire engine controllers and control techniques are described. In some preferred embodiments, a skip fire engine controller is provided that includes a firing fraction calculator, an engine settings controller, a firing fraction adjuster and a firing controller. The firing fraction calculator determines a reference firing fraction indicative of a firing fraction suitable for delivering a desired engine output at a reference working chamber firing output. The engine settings controller is arranged to set selected engine settings. The firing fraction adjuster determines an adjusted firing fraction that scales the reference firing fraction appropriately such that the engine will deliver the desired engine output at the current engine settings even when the actual working chamber firing outputs do not equal the reference working chamber firing output. The firing controller direct workings chamber firings in a skip fire manner that delivers the adjusted firing fraction.