In our previous research, two-stage anaerobic co-fermentation (TSAC) treating lipid-extracted microalgae waste (LEMW) mixed with food waste leachate (FWL) was successfully designed to recover the additional energy (H2 and CH4) while mitigating the inhibition of leftover chloroform (CF). This study aimed to elucidate the change in the microbial community and their association with the CF degradation in the TSAC. 90% of CF was dechlorinated in the acidogenic reactor of TSAC when LEMW was fed with FWL at a ratio of 40:60. The results of microbial analysis clearly showed that Dehalobacter (5.3%) played the role in dehalorespiration while Clostridium (8.9%) and Enterobacter (3.6%) promoted cometabolic dechlorination. In contrast, the microbial consortia were completely inhibited by CF when LEMW was fed without FWL. In the methanogenic reactor of TSAC, increased Methanosarcina (57.8%), Methanobacterium (10.4%), and Methanosaeta (8.6%) were observed. Those were involved in successful conversion of acetate and H2 into CH4.