Removal of multiple contaminants from flue gas streams in a single process step offers the potential to lower the cost of emissions reduction technologies. An example is the CS-Cap process, developed by CSIRO, which removes both the SO2 and CO2 from combustion flue gases. In order to further develop this process, a rate based simulation is required of not only the CO2 capture section, but also the absorption of SO2 into aqueous amine absorbents. ProTreat® simulation software was used to simulate CSIRO’s Loy Yang CO2 capture pilot plant. This pilot plant has previously been used for proof-of-concept operation of the CS-Cap process. The model simulates various scenarios and flue gas conditions to determine the effect on the operating requirements of the SO2 capture stage. It reveals that the recirculating absorbent flow rates required in the SO2 capture loop are of similar magnitude to those required in the CO2 capture stage. Manipulating the operating parameters of the SO2 capture section will affect the properties, particularly sulfate concentration, of the slip stream sent for disposal/treatment. This could potentially allow the properties of the waste stream to be tailored for the particular downstream treatment used. In addition, condensation of water from the inlet flue gas stream is identified as an issue requiring further investigation.