Anaerobic digestion, a promising technology for waste utilization and bioenergy generation, is a suitable approach to convert the shrimp waste to biomethane, reducing its environmental impact. In this study, shrimp chaff (SC) was co-digested corn straw (CS), wheat straw (WS), and sugarcane bagasse (SB). In co-digestion, SC enhanced biomethane production of CS by 8.47-fold, followed by SC+WS (5.67-folds), and SC+SB (3.37-folds). SC addition to agricultural biomass digestion also promoted the volatile solids removal up to 85%. Microbial community analysis of SC and CS co-digestion presented the dominance of phylum Bacteroidetes, Firmicutes, Proteobacteria, and Euryarchaeota. Proteolytic bacteria were dominant (18.02%) during co-digestion of SC and CS, with Proteiniphilum as major bacterial genera (14%) that converts complex proteinaceous substrates to organic acids. Among the archaeal community, Methanosarcina responsible for conversion of acetate and hydrogen to biomethane, increased up to 70.77% in SC and CS digestion. Addition of SC to the digestion of agricultural wastes can significantly improve the biomethane production along with its effective management to reduce environmental risks.