The comparison among microbial interactions during the stable performance of anaerobic digestion (AD) and the process disturbances is still lack and could limit the prediction of process failure and the possible recovery. This study aimed at characterizing the process performance and microbial communities’ profiles during the stable and disturbed states of long-term thermophilic AD process fed with agro-food wastes. The disturbances were induced in two stages, firstly under a stepwise increase of organic loading rate (OLR), and then through the reduction in hydraulic retention time (HRT). Volatile fatty acids (VFAs) only accumulated (4730 mg L-1) when OLR increased to 17 g VS L-1 d-1, and consequently methane yield deteriorated by 47%, implying process overloading and thus AD process was partially inhibited. Process disturbances led to 30% reduction in relative abundance of Defluviitoga and Methanoculleus which were partially displaced by Clostridium and Methanomassiliicoccus, implying that the process acidification immediately reflected on microbial profile and the microbes were functionally redundant. Microorganisms’ washout was the main reason behind methane yield drop under finite digestion time (1.5d). Microbial profiles shaping showed the robustness of AD process due to the functionally redundant microorganisms and could be strategically used to control and optimize AD process.