A fuel cell system for removing CO2 from anode exhaust gas includes a fuel cell having an anode that outputs anode exhaust including H2, CO, CO2, and water; a shift reactor that receives a first portion of the anode exhaust and performs a water-gas shift reaction to produce an output stream primarily including H2 and CO2; an anode gas oxidizer (AGO); and an absorption system including an absorber column that absorbs the CO2 from the output stream in a solvent and outputs a resultant gas including H2 and a hydrocarbon that is at least partially recycled to the anode, and a stripper column that regenerates the solvent and outputs a CO2-rich stream. The AGO is configured to oxidize at least a portion of the CO2-rich stream and an AGO input stream that includes one of a second portion of the anode exhaust or a portion of the output stream.