Microalgae-based advanced wastewater treatment has gained momentum due to the possibility of recovering nutrients for the production of fertilizers, biofuels and fine chemicals from microalgal biomass. The objective of this study is to evaluate the effect of different fouling control strategies on the development of Chlorella vulgaris in a membrane photobioreactor (AMPMBR) treating a secondary wastewater effluent. The experimental results showed a decrease in the fouling rate (bar/hours) of 50% for backwash and relaxation and 60% for nitrogen bubble scouring. Additionally, in-situ non-destructive real time monitoring was employed to visualize and assess the change in morphology of the algae formed on the membrane surface. The use of fouling mitigation led to substantial changes in the biomass morphologies impacting the performance of the AMPMBR. The lowest biomass deposition (5–10 µm) was observed when nitrogen bubble scouring was employed, while the application of relaxation led to the thickest (180 µm), most heterogeneous and porous structure. The use of backwash led to a partial temporary biomass detachment from the membrane surface. This study, provided a better understanding of the impact of fouling mitigation strategies on the biomass formed on the membrane of AMPMBR.