Abstract: A system to protect an after treatment system from the effects of hydrocarbon accumulation on a catalyst. An engine system microprocessor using software estimates the amount of hydrocarbon accumulation on the after treatment system based on engine system parameters and other parameters. The accumulated hydrocarbons can cause an exothermic event if the catalyst temperature is allowed to ramp up too quickly. Similarly, accumulated hydrocarbon can temporarily reduce after treatment system performance. In the case of SCR, the microprocessor can control a reductant injector to modulate the amount of reductant being injected into the after treatment system to control the amount of ammonia slip. Alternatively or in addition to, the microprocessor can communicate with proper electronic control modules to modulate the engine system parameters such as engine speed, fuel, and back pressure to control engine exhaust flow temperature during operation of the engine system.