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Abstract Resource recovery and prevention of environmental pollution are key goals for sustainable development. It is widely reported that agro-industrial activities are responsible for the discharge of billions of liters of wastewater to the environment. Anaerobic digestion of these energy rich agro-industrial wastewaters can simultaneously mitigate environmental pollution and recover embedded energy as methane gas. In this study, an assessment of mono- and co-digestion of cheese whey wastewater (CWW) and poultry slaughterhouse wastewater (PSW) was conducted in 2.25-L lab-scale anaerobic digesters. Treatment combinations evaluated included CWW (R1), PSW (R2), 75:25 CWW:PSW (R3), 25:75 CWW:PSW (R4), and 50:50 CWW:PSW (R5). The digestion efficiencies of the mixed wastewaters were compared to the weighted efficiencies of the corresponding combined mono-digested samples. R4, with a mixture of 25% CWW and 75% PSW, achieved the greatest treatment efficiency. This corresponded with an average biodegradability of 84%, which was greater than for R1 and R2 at 68.5 and 71.9%, respectively. Similarly, R4 produced the highest average cumulative methane value compared to R1 and R2 at 1.22× and 1.39× for similar COD loading, respectively. The modified Gompertz model provided the best fit for the obtained methane production data, with lag time decreasing over progressive treatment cycles. PCoA and heatmap analysis of relative microbial abundances indicated a divergence of microbial communities based on feed type over the treatment cycles. Microbial community analysis showed that genusPetrimonasattained the highest relative abundance (RA) at up to 38.9% in the first two cycles, then subsequently decreased to near 0% for all reactors.Syntrophomonaswas highly abundant in PSW reactors, reaching up to 36% RA.Acinetobacterwas present mostly in CWW reactors with a RA reaching 56.5%. The methanogenic community was dominated byMethanothrix(84.3–99.9% of archaea). The presence of phosphate andAcinetobacterin CWW feed appeared to reduce the treatment efficiency of associated reactors. DespiteAcinetobacterbeing strictly aerobic, previous and current results indicate its survival under anaerobic conditions, with the storage of phosphate likely playing a key role in its ability to scavenge acetate during the digestion process.