Microalgae have the potential for biogas upgrading and digestate management as a downstream technology of anaerobic digestion. Through the acclimation to typical swine manure digestate with 1630 mg/L NH4-N, semi-continuous microalgae treatment was operated for biogas treatment with up to 4000 ppm H2S. Control of pH was necessary at high biogas to digestate liquid (G/L) ratios above 1 mol/L or 25:1 v/v (1 atm, 25 °C). Biogas decarbonation and desulfurization were achieved simultaneously with G/L ratios from 0.04 to 1.63 mol/L (1:1 to 40:1 v/v, at 1 atm, 25 °C), and nearly all methane remained in the upgraded biogas. Ammonia nitrogen as high as 930 mg NH4-N/L/d was removed at higher G/L ratios. The removed carbon and nitrogen were captured and assimilated into biomass at rates up to 13 g CO2/L/d and 540 mg NH4-N/L/d, respectively. The optimal phosphorus assimilation rate was 49 mg PO4-P/L/d obtained at the G/L ratio of 1.02 mol/L. These findings demonstrate that microalgal can treat high-H2S biogas and high-NH4-N digestate within a broad range of G/L ratios, including ratios that are similar to biogas and digestate generation ratios from swine manure digesters.