Impact of strip gas composition on side stream ammonia stripping, a technology aiming at the reduction of high ammonia levels in anaerobic reactors, was investigated. Evaluation of the effect of oxygen contact during air stripping showed a distinct, though lower than perceived, inhibition of anaerobic microflora. To circumvent, the feasibility and possible constraints of biogas and flue gas as alternatives in side stream stripping were studied. Experiments, with ammonia bicarbonate model solution and digestate, were conducted. It was demonstrated that the stripping performance is negatively correlated to the CO2 level in the strip gas with a progressive performance loss towards higher concentrations. In contrast to biogas with its high CO2 content, the efficiency reduction observed for flue gas was significantly less pronounced. The later provides the additional benefit that its high thermal energy can be re-utilized in the stripping unit and it is therefore considered a viable alternative for air.