A control system and method of predicting how a machine will respond to occasional or periodic service, and adjusting the machine accordingly to account for the change in machine behavior due to the service, mitigates transients in machine performance. A prediction of the service effect is fed forward to the existing control system just prior to the occurrence of service in order to compensate for the service effect. This prediction is continually updated and refined using subsequent measurements of the effect of service on machine performance. More specifically, a controller monitors the process output variables indicative of the machine performance and adjusts machine inputs to achieve a desired level of machine performance. The controller monitors the process output variables indicative of the machine performance prior to, during, and immediately after the service and adjusts the machine inputs to compensate for the transients.