The study investigated anaerobic treatment of high strength effluents polluted with Cr (VI), in hybrid anaerobic reactor (HAR) developed at IIT Delhi. Performance was evaluated by a time-course analysis, conducted for two different phases i.e. granulation and treatment, linked with the microbiome dynamics. During granulation higher methane was generated while, it was substantially hindered during the second phase. Genera with degradation abilities were identified viz- Methanobacterium, Clostridium, Halorhodospira, Oscillibacter, Pseudomonas, Stenotrophomonas, Methylobacterium. Bioaugmentation with such keystone species will help maintain microbially active centers. The findings indicated extreme bacterial reduction (R = −0.986, CI = 0), coupled with hindered acidogenesis. Methanomicrobiales prevailed in the treating phase while, aceticlastic families flourished during granulation. Further, non-metric multidimensional scaling, principal component analysis explored the interactions between environmental, microbial and chemical variables. With the focus on the applicability of anaerobic treatment with tannery-type of effluents, the study provided a comprehensive investigation for superior monitoring.