An engine controller determines the cost of operating a combustion engine and the cost of operating an emissions after-treatment device. Accordingly, the engine controller adjusts parameters for operation of the engine and the after-treatment device to ensure cost-effective use of the engine and the after-treatment device while complying with exhaust emissions requirements. In particular, the engine controller receives the price of fuel consumed by the engine and the price of reductant used by the after-treatment device to determine the respective cost of operation. Specifically, the fuel is diesel fuel used in a diesel engine; the reductant is urea use in a urea-based Selective Catalytic Reduction (SCR) system; and the regulated exhaust emissions is nitrogen oxide (NOx) emissions. The engine operating parameters may include cooled exhaust gas recirculation airflow, fuel injection timing, fuel injection pressure, and air-to-fuel ratio. The SCR system operating parameters may include the volume of urea injected.