Novel operational strategies to reduce the O 2 concentration in the upgraded biogas were evaluated in a 180 L algal–bacterial photobioreactor interconnected to a 2.5 L external absorption column during the simultaneous treatment of diluted anaerobically digested or raw vinasse and biogas upgrading. The lowest biomethane O 2 levels (0.7 ± 0.2%) were recorded when raw vinasse was fed directly into the absorption column, which resulted in CO 2 and H 2 S removals from biogas of 72 ± 1% and 100 ± 0%, respectively. Process operation at a Hydraulic Retention Time (HRT) of 7 d under the above configuration also supported the maximum total carbon, nitrogen and phosphorus removals of 72 ± 4%, 74 ± 3% and 78 ± 5%, respectively. Biomass productivity ranged from 11.4 ± 1.8 to 13.5 ± 2.2 g m − 2 d − 1 during microalgae cultivation in diluted anaerobically digested vinasse, while this productivity increased to 16.9 ± 0.7 g m − 2 d − 1 when feeding diluted raw vinasse. The good settling characteristics of the algal–bacterial flocs resulted in an average harvesting efficiency of 98.6 ± 0.5% at a HRT in the settler of 23 min, regardless of the treated vinasse. The morphological and molecular characterization of the microbial communities showed a high microalgae diversity and bacterial species richness, regardless of the operational conditions (Shannon–Wiener indices ranging from 2.8 to 3.3).