A method of controlling SO.sub.3 flue gas concentration in a combustion process utilizing a SCR using a sulfurous fuel, the method steps including: providing a combustion system with low NOx burners and SCR; partially combusting the fuel in a first stage to create a reducing environment; maintaining the reducing environment for a sufficient time period such that SO.sub.3 is reduced to SO.sub.2 to achieve a desirable level of SO.sub.3; combusting the remainder of the fuel and combustion intermediates in a second stage with oxidizing environment; reducing the remaining NOx with the SCR; thereby reducing emissions NOx.