As a result of self-heating in anaerobic digesters when using energy crops in the feedstock, the influence of temperature on the digestion process came back into focus. The aim of this study was to investigate the impact of such temperature increases on process stability. Furthermore, different strategies for the transition from mesophilic to thermophilic conditions and the resulting methane yields at different temperature levels were evaluated. Two main effects were identified with different bio-slurries from agricultural biogas plants: (1) a failure of methane production connected to changes in the microbial community; and (2), a slow but continuous accumulation of propionic acid, though without an immediate effect on methane production. All strategies for increasing the operating temperature showed negative effects on digester performance, some with serious economic consequences for the operator. It was shown that methane yields at different temperature levels in the mesophilic and sub-thermophilic ranges are similar.