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 NH4+-N > 100 mg/L, but NO3--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 NH4+-N to NO3--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, NH4+-N, NO3--N and PO43--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% NH4+-N and > 99% PO43--P could be continuously removed from 10% digestate. Although NH4+-N removal in the process was mainly through nitrification, total nitrogen removal was > 75% at steady state. The effects of lower NH4+-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.