Operating temperature significantly affects biogas output, process stability, and microbial communities involved in anaerobic digestion. There are several unanswered questions regarding how microbial communities adapt in correlation with biogas production performance, especially when a digester fails to maintain thermophilic conditions. In this study, long-term lab-scale anaerobic digestion was carried out using two fed-batch reactors at 55°C, with subsequent decreases in temperature to 48°C and 45°C. Within the first month of incubation, methane (CH 4 ) production increased by approximately 11.18% following a reduction in temperature from 55°C to 48°C. However, the methane production decreased by 33% after the temperature was downshifted to 45°C. Despite the difference in methane production, the thermophilic methanogen population in both reactors declined significantly in the first month with a temperature decrease. After two months of incubation, these methanogenic communities recovered faster at 48°C than at 45°C, which was highlighted by the rapid colonization of Methanosaeta, Methanobacterium, and Methanothermobacter. Notably, Methanosaeta was the most abundant methanogen under all temperature conditions, indicating its thermotolerance.