A method of controlling a skip-fire cylinder deactivation system of an engine system is provided. The method includes a controller deactivating a cylinder of the engine system to operate the engine system in a skip-fire mode. The method further includes determining a temperature of an injector tip nozzle associated with the cylinder and comparing the temperature of the injector tip nozzle to a threshold a temperature. In response to determining that the temperature of the injector tip nozzle is greater than the threshold temperature, the cylinder is activated by the controller.