Abstract Microalgae can be manipulated to accumulate certain cellular compounds of interest without the need for genetic modification - simply by controlling growth parameters such as nitrogen (N). Therefore, A. obliquus was batch-cultivated in a sleevebag photobioreactor system in N-deprived and N-rich medium to test the effect of N-status on CH 4 yield under anaerobic digestion. Two different dewatering methods, i.e., centrifugation and sedimentation were applied to each resulting biomass. For the N-deprived biomass, cellular protein content dropped by 42–49%, and lipids increased up to 20% relative to the N-rich biomass. The highest CH 4 yields were achieved with N-deprived, sedimented biomass (391 Nm 3 t − 1 VS = normalized gas volume in m 3 corrected to norm temperature and pressure per unit volatile solids), followed by N-rich sedimented biomass (361 Nm 3 t − 1 VS). Centrifugation led to lower CH 4 yields, where N-deprived biomass achieved 280 compared to 200 Nm 3 t − 1 VS for N-rich microalgae. Our data indicate that valuable organic material was lost to the supernatant during the centrifugation step. We conclude that not only the N-status of cultivation, but also the biomass dewatering method has an instrumental effect on CH 4 yield of microalgal biomass in anaerobic digestion.