This study examines the potential of the mixed-culture microalgal consortia enriched from aerobic sludge (AeS) and anaerobic sludge (AnS) with regard to nutrient removal and biomass production from four different anaerobic digestion (AD) effluents. Both the inocula achieved the complete removal of the NH4+-N (initial concentration of 40 mg/L) within 14 days from all the effluents. The AeS cultures showed faster and greater microalgal growth, although the NH4+-N removal rate was comparable or higher in the case of the AnS cultures. Further, the AeS and AnS cultures showed significantly different lipid production characteristics in terms of the fatty acid composition and the response to nitrogen deficiency. Nitrogen starvation caused changes in the microbial community structures in all the experimental cultures, which may have influenced the lipid metabolism and the microalgal growth. The overall results suggest that both the inocula exhibit good potential with regard to the treatment of AD effluents.