The present study was to investigate the feasibility of carrying out effective microalgae cultivation and high-rate tertiary wastewater treatment simultaneously in a vertical sequencing batch photobioreactor with small areal footprint, suitable for sustainable urban microalgae production. For 15 consecutive days, Chlorella sorokiniana was cultivated in synthetic wastewater under various trophic conditions. A cycle of 12-h heterotrophic: 12-h mixotrophic condition produced 0.98 g l−1 d−1 of algal biomass in tandem with a 94.7% removal of 254.4 mg l−1 C-acetate, a 100% removal of 84.7 mg l−1 N-NH4 and a removal of 15.0 mg l−1 P-PO4. The cells were harvested via cost-effective chitosan flocculation with multiple dosing (3 times) applying established chitosan:cell ratio (1:300 w/w) and pH control (6.3–6.8). Reproducible flocculation efficiencies of greater than 99% and high-concentration algal broths (>20% solids) were achieved.