As microalgae have the ability to simultaneously remove nutrients from wastewater streams while producing valuable biomass, microalgae-based wastewater treatment is a win–win strategy. Although recent advances have been made in this field in lab conditions, the transition to outdoor conditions on an industrial scale must be further investigated. In this work an outdoor pilot-scale membrane photobioreactor plant was operated for tertiary sewage treatment. The effects of different parameters on microalgae performance were studied including: temperature, light irradiance (solar and artificial irradiance), hydraulic retention time (HRT), biomass retention time (BRT), air sparging system and influent nutrient concentration. In addition the competition between microalgae and ammonium oxidising bacteria for ammonium was also evaluated. Maximum nitrogen and phosphorus removal rates of 12.5 ± 4.2 mgN·L−1·d−1 and 1.5 ± 0.4 mgP·L−1·d−1, respectively, were achieved at a BRT of 4.5 days and HRT of 2.5 days, while a maximum biomass productivity of 78 ± 13 mgVSS·L−1·d−1 (VSS: volatile suspended solids) was reached. While the results obtained so far are promising, they need to be improved to make the transition to industrial scale operations feasible.