In one aspect, a method for mitigating detonation in a skip fire engine control system is described. The working chambers of the engine are operated in a skip fire manner to deliver a desired torque. One or more detonations are detected in the engine. In response to the detection of the one or more detonations, the spark timing for one or more of the working chambers is retarded. Additionally, the firing fraction used to operate the engine is increased. The increase in the firing fraction helps to compensate for torque lost due to the retarding of the spark timing.