Increasing worldwide milk manufacturing and dairy processing resulted in producing more effluents, and thus effective management of wastewater is now the most important issue. This study used a new design of a pilot plant-scale hybrid anaerobic labyrinth-flow bioreactor (AL-FB) to increase the efficiency of anaerobic biodegradation and biogas productivity and improve anaerobic microflora performance. In addition, effluent recirculation was used to boost the treatment of dairy wastewater. Metagenomic analyses of the anaerobic microbial community were performed. It was found that an organic loading rate (OLR) of 4.0–8.0 g COD/L·d contributed to the highest CH4 yield of 0.18 ± 0.01–0.23 ± 0.02 L CH4/g COD removed, which corresponded to a high COD removal of 87.5 ± 2.8–94.1 ± 1.3%. The evenest distribution of the microorganisms’ phyla determined the highest biogas production. In all tested samples, Bacteroidetes and Firmicutes abundance was the highest, and Archaea accounted for about 4%. Metagenomic studies showed that methane was mainly produced in acetoclastic methanogenesis; however, higher OLRs were more favorable for enhanced hydrogenotrophic methanogenesis. Effluent recirculation enhanced the overall treatment. Thus, at OLR of 10.0 g COD/L·d, the highest COD removal was 89.2 ± 0.4%, and methane production yield achieved 0.20 ± 0.01 L CH4/g COD removed, which was higher by 25% compared to the achievements without recirculation.