This work assesses the capacity of a microalgae-based system to remove three highly to medium polar pesticides typically found in freshwater: acetamiprid, bentazone, and propanil. Degradation of the pesticides was firstly studied individually at batch lab-scale reactors and abiotic and heated-killed controls were employed to clarify their removal pathways. At lab-scale, propanil and acetamiprid were completely removed after 7 days whereas bentazone was not removed. Four and two transformation products (TPs) were generated in the biodegradation process for acetamiprid and propanil, respectively. Then, the simultaneous removal of the pesticides was assessed in an outdoor pilot photobioreactor, operated with a hydraulic residence time of 8 days. During the steady-state, high removal efficiencies were observed for propanil (99%) and acetamiprid (71%). The results from batch experiments suggest that removal is mainly caused by algal-mediated biodegradation. Acetamiprid TPs raised throughout the operational time in the photobioreactor, while no propanil TP was detected at the pilot-scale. This suggests complete mineralization of propanil or residual formation of its TPs at concentrations below the analytical method detection limit. Aiming at biomass valorization, diverse microalgae harvesting methods were investigated for biomass concentration, and the effect of residual pesticides on the biogas yield was determined by biochemical methane potential tests. Anaerobic digestion was not inhibited by the pesticides as verified by the digestion performance. The results highlight the potential of microalgae-based systems to couple nutrient removal, biomass production, micropollutant biodegradation, and biofuel production.