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Highlights • Microalgae growth was inhibited at NH 4 +-N concentrations above 100 mg/L. • Microalgae growth in digestate was suppressed by high NH 4 +-N and competing microbes. • Nitrification based pre-treatment was effective in alleviating NH 4 +-N toxicity. • Excellent nitrogen and phosphorus recovery from nitrified digestate by microalgae. • Integrated nitrification and algae cultivation possible using membrane bioreactors. Abstract High ammonium concentration is considered a major challenge in cultivating autotrophic microalgae in anaerobic digestate. In this research, the feasibility of applying nitrification as pretreatment to alleviate ammonium toxicity on microalgae was investigated. Batch experiments conducted in synthetic medium showed that microalgae growth was inhibited at NH 4 +-N > 100 mg/L, but NO 3 −-N was benign at concentrations as high as 350 mg/L. Microalgae growth in 2–50% digestate (v/v) was also affected adversely by invading heterotrophic microorganisms. Digestate pre-treatment using activated sludge mitigated these challenges by converting NH 4 +-N to NO 3 −-N, and reducing organics content in the digestate. Microalgae exhibited excellent growth and nutrients removal in nitrified digestate (5–30% mixed with municipal wastewater) in batch mode. For example, COD, NH 4 +-N, NO 3 −-N and PO 4 3−-P removal in 10% digestate using two-stage bacterial-microalgal process were 87%, 100%, 30% and 77%, respectively. In continuous mode, using a microalgae-based membrane photobioreactor (MPBR) operating downstream to membrane bioreactor (MBR), 91% COD, 97% NH 4 +-N and >99% PO 4 3−-P could be continuously removed from 10% digestate. Although NH 4 +-N removal in the process was mainly through nitrification, total nitrogen removal was >75% at steady state. The effects of lower NH 4 +-N toxicity in the MPBR was also manifested in terms of high microalgae biomass accumulation of about 5 g/L. These results indicate that nitrification can be a promising pretreatment for anaerobic digestate for use in microalgae cultivation. [ABSTRACT FROM AUTHOR]