The objective of this study was to delineate the effects of different coffee processing residues on the anaerobic microbes and corresponding digestion performance. The results elucidated that mucilage-rich feed enhanced the accumulation of methanogens, which consequently led to better digestion performance of biogas production. Fifty percent more methane and up to 3 times more net energy (heat and electricity) output were achieved by the digestion of the mucilage-rich feed (M3). The microbial community and statistical analyses further elucidated that different residues in the feed had significant impact on microbial distribution and correspondingly influenced the digestion performance.