This study investigated nutrient removal from anaerobic digestion effluent by cultivating mixed-culture microalgae enriched from anaerobic sludge under different pH conditions: R_UC (uncontrolled), R_7–8 (maintained at 7–8), and R_<8 (maintained below 8). Significant amounts of NH₄⁺-N were lost by volatilization in R_UC cultures due to increased pH values (≤8.6) during the early period of cultivation. The pH control strategies significantly affected the biological NH₄⁺-N removal (highest in R_7–8), microalgal growth (highest in R_7–8), biomass settleability (highest in R_<8), and microalgal growth relative to bacteria (highest in R_<8) in the cultures. Parachlorella completely dominated the microalgal communities in the inoculum and all of the cultures, and grew well at highly acidic pH (<3) induced by culture acidification with microalgal growth. Microalgae-associated bacterial community structure developed very differently among the cultures. The findings call for more attention to the influence and control of pH changes during cultivation in microalgal treatment of anaerobic digestion effluent.