Monitoring of anaerobic digestion process is essential for achieving efficient and stable performance, thus requiring identification of effective stability indicators. The response of two experimental, continuously stirred tank reactors under mesophilic condition (fed with pig manure)was investigated to analyze the perturbation of organic and hydraulic overloading, and low-temperature shock. The pH was stably maintained in the range of 7.2–7.7, regardless of the presence of most simulated perturbation situations. Monitoring of biogas production and composition is important to reflect the current state of biogas process, but cannot predict the imbalance in the system. Accumulation of total VFAs up to 21,718 mg/L was observed under the organic overloading condition (rapid increase of the organic loading rate of pig manure from 3 g VS/L/d to 9 g VS/L/d), but not for other perturbations. The ratio of propionate to acetate and that of intermediate alkalinity to partial alkalinity are rapidly altered in response to all perturbations, indicating their potential to function as stability indicators. However, the determination of the ratio of intermediate alkalinity to partial alkalinity can be performed by simple titration methods and be easily applied to actual projects without significant investment in advanced equipment and skilled operators.