Respirometric techniques are useful tools to evaluate bacterial activities in activated sludge processes due to their fast execution and the possibility to obtain several kinetic parameters from a single test. Using such techniques in microalgae-bacteria consortia treating wastewater could allow a better understanding of mutual interactions between the microbial populations as a function of environmental parameters. This work aims at developing and testing a novel experimental respirometric protocol to determine oxygen uptake rates and oxygen production rates by a microalgae-bacteria consortium. The defined protocol is characterized by alternating light/dark regimes and by dosing substrates/inhibitors to selectively activate/inactivate microalgal and bacterial metabolisms. The protocol was then applied on microalgal and bacterial consortia, which were grown on the liquid fraction of black water from biogas plants fed on agricultural and municipal waste sludge. Results elucidate the presence and activity of microalgae and nitrifying bacteria in the tested systems, suggesting that the respirometric tests could be included into monitoring procedures of photobioreactors/algal ponds.