A microalgae–bacteria system was used for dairy industry wastewater treatment in sequenced batch mode in a photobioreactor. The research investigated the influence of two light intensities: 360 and 820 μmol m−2s−1 on treatment performances, microalgal cell recovery and dynamics of the protozoan community. Results showed that the light intensity of 360 μmol m−2s−1 was found to be insufficient to support photosynthetic activity after the increase of bacterial biomass leading to the decrease of organic matter and ammonium removal efficiencies from 95 to 78% and 95 to 41%, respectively. Maximum microalgal cells recovery was about 63%. Continuous modification in the protozoan community was also noticed during this test. Increasing the light intensity to 820 μmol m−2s−1 led to better microalgal cells recovery (up to 88%) and improved treatment performances. However, the decrease of protozoan richness to small flagellates and free-swimming ciliates was noticed. Moreover, the developed protozoan trophic network was found to be different from that identified in the conventional activated sludge system. The study emphasized that high increase of bacterial biomass promoted in nutrient- and organic matter-rich wastewater can strongly affect the treatment performances as a result of the shadow effect produced on the photoautotrophic microalgae aggregates.