A novel coupling process using an aerobic bacterial reactor with nitrification and sulfur–oxidization functions followed by a microalgal reactor was proposed for simultaneous biogas desulfurization and anaerobic digestion effluent (ADE) treatment. ADE nitrified by bacteria has a potential to be directly used as a culture medium for microalgae because ammonium nitrogen, including inhibitory free ammonia (NH3), has been converted to harmless NO3−. To demonstrate this hypothesis, Chlorella sorokiniana NIES-2173, which has ordinary NH3 tolerance; that is, 1.6 mM of EC50 compared with other species, was cultivated using untreated/treated ADE. Compared with the use of a synthetic medium, when using ADE with 1–10-fold dilutions, the specific growth rate and growth yield maximally decreased by 44% and 88%, respectively. In contrast, the algal growth using undiluted ADE treated by nitrification–desulfurization was almost the same as with using synthetic medium. It was also revealed that 50% of PO43− and most metal concentrations of ADE decreased following nitrification–desulfurization treatment. Moreover, upon NaOH addition for pH adjustment, the salinity increased to 0.66%. The decrease in metals mitigates the bioconcentration of toxic heavy metals from wastewater in microalgal biomass. Meanwhile, salt stress in microalgae and limiting nutrient supplementation, particularly for continuous cultivation, should be of concern.