The CSTR process has previously not been successfully applied to treat coffee residues under thermophilic temperature and long term operation. In this experiment, the CSTR was fed with mixture substrate (TS∼70g/L) of coffee grounds, coffee wastewater, milk waste and municipal sludge and it was operated under 55°C for 225days. A steady state was achieved under HRT 30days and OLR 4.0kg-COD/m(3)/d. However, there was an 35days inhibition with VFA accumulation (propionic acid 700-1900mg/L) when doubling the OLR by shortening HRT to 15days. But, an addition of microelements and sulfate (0.5g/L) in feedstock increased reactor resilience and stability under high loading rate and propionic acid stress. Continuous monitoring of hydrogen in biogas indicated the imbalance of acetogenesis. The effectiveness of comprehensive parameters (total VFA, propionic acid, IA/PA, IA/TA and CH4 content) was proved to manage the thermophilic system.