The performance of a pilot high rate algal pond (HRAP) interconnected with a biogas absorption column during the simultaneous upgrading of biogas and treatment of digestate was evaluated under two innovative biogas and nutrient supply strategies. Process operation with biogas supply during the night at a liquid recirculation/biogas ratio of 0.5 to prevent N-2 and O-2 stripping resulted in a biomethane complying with most international regulations for injection into natural gas grids (99.1 +/- 1% CH4, 0.5 +/- 0.2% CO2, 0.6 +/- 0.5% N-2 and 0.07 +/- 0.08% O-2). The potential of this technology to remove methyl mercaptan (MeSH), toluene and hexane from biogas (typically present at trace levels) was assessed, for the first time, with removal efficiencies under steady-state correlating with pollutant hydrophobicity (7 +/- 7% for hexane, 66 +/- 4% for MeSH and 98 +/- 1% for toluene). Finally, the supply of digestate during the dark period shifted both microalgae population structure and biomass composition in the HRAP without a significant impact on biomethane quality. Overall, the removal of nitrogen and phosphorous from digestate in the HRAP was almost complete (96-99%) regardless of the nutrient supply strategy.