The operating temperature in anaerobic digestion strongly affects biogas yield, process stability and the potential for process optimisation. However, many questions remain on how to manage process operation for optimized microbial community adaptation following temperature changes. A long-term anaerobic digestion experiment was conducted to determine temperature-related issues in operative full-scale biogas plants and to evaluate optimisation potential and links to microbial community structure and responses. Four digesters fed household and slaughterhouse waste were operated in sets of two, at 37 degrees C or 52 degrees C, followed by a gradual increase or decrease in temperature in one digester in each set. Stability and flexibility of the digesters were then assessed by step-wise increases in organic loading rate (OLR) from 3 to 7 g VS/(L day), concurrently with decreased hydraulic retention time from 33-40 days to 14-17 days. Transition of operating temperature regime was possible, irrespective of starting temperature. However, slight temporary instability occurred at 42-44 degrees C and for the thermophilic to mesophilic process a period of adaptation was required to overcome this imbalance. The digesters with constant temperature and the mesophilic-to-thermophilic digester remained stable at the target OLR, demonstrating considerable optimisation potential for the large-scale biogas plants investigated. However, the digester that was changed from thermophilic to mesophilic conditions failed at 6 g VS/(L day). Comparisons of biological and chemical parameters suggested that this failure was caused by a lag in resilience of the acetate and propionate-degrading populations inherited from the community shaped by initial operation in thermophilic conditions. Taken together, these results demonstrate that the existing biogas plants are operating below capacity and that, depending on temperature, the annual energy production could be increased from 26-28 to 59-65 GWh through increasing OLR from 3 to 7 g VS/(L day). However, the results also highlight the importance of careful management and the risks when applying strategies not fully evaluated for the specific system. To our knowledge, this is the first study to demonstrate process performance, optimisation potential and microbial community adaptability to temperature changes in continuously fed anaerobic digesters under both increasing and decreasing operating temperature. The results could be used to guide operation management under temperature changes and increasing OLR in industrial-scale biogas processes.