This study investigated the algal and prokaryotic community structure in an outdoors pilot High Rate Algal Pond (HRAP) that was simultaneously used for the treatment of high-strength wastewater and biogas upgrading. The algal and prokaryotic diversity was analyzed and correlated with biological and environmental parameters, and process quality indicators. The results obtained showed that the dominance of a versatile and resistant algae, such as Chlorella vulgaris, which is tolerant to high NH4+ and CO2 concentrations, concomitant to a specific prokaryotic population allowed for the obtention of biomethane with 95.2 ± 0.7% CH4, 1.4 ± 0.1% CO2 and no H2S. The bacterial community, fostered by the algal population, the light hours, and photoperiod had an important role on both biogas upgrading, through O2 and H2S elimination, and wastewater treatment. While the algal population was involved in the elimination of the ammonium of the wastewater through assimilation, the bacterial population was the main factor responsible for organic carbon, nitrate and phosphate removal, as well as nitrification. The low oxygen concentrations at night promoted bacterial denitrification, increasing the nitrite concentration in the treated wastewater. Through these findings, this research encourages photosynthetic biogas upgrading combined with wastewater treatment in HRAPs using an inoculum composed of a dominant microalgae, and an enriched prokaryotic population of aerobic chemo-organoheterotrophs, aerobic nitrifiers, and sulfur bacteria. Unlike the bacterial consortium in this study, this designed consortium can avoid the accumulation of nitrite in the cultivation broth and reduce the content of oxygen in the produced biomethane.