A system and method for operating an engine having ionization signal sensing include detecting plug fouling and controlling the engine using progressively more aggressive control strategies if the fouling condition persists. A first control strategy may be used when the number of engine starts or running time are below corresponding thresholds and a second strategy otherwise. The first strategy may employ progressively more aggressive control procedures to eliminate spark plug deposits that may include repetitive sparking, exhaust cycle sparking, increasing engine loading, advancing spark timing, increasing air/fuel ratio, and increasing idle speed, for example. The second strategy may include similar corrective actions employed in a different order and/or to a lesser degree in an attempt to eliminate plug fouling without any noticeable change in engine operation or performance as perceived by the vehicle operator. The control strategies may be applied to individual cylinders, cylinder banks, or all cylinders.