Although anaerobic digestion (AD) is a rather mature technology, poor anaerobic digester performance and system failure are still frequent around the world. Most of these problems occur as a result of inadequate operational management and lack of process control. Digester upsets are usually temporary, and in most cases can be solved by taking simple measures, such as adjusting the influent co-digestion ratio and/or the frequency of influent pumping. If prompt and adequate measures are not taken, the digester operation will eventually fail. Recovery of a digester can take several months, during which, energy generation and waste treatment are not possible, resulting in increased operational costs for the farm. The importance of well-trained and qualified personnel to operate AD systems and properly control and monitor the process is essential, not only to prevent digester upsets and potential system failures, but also to ensure efficient organic waste stabilization and constant and stable biogas production. Analytical laboratories were installed on selected farm-based anaerobic digester systems in NYS to regularly monitor key process parameters and to evaluate performance and stability of the operations. Preliminary results of the monitoring confirmed that analytical labs are essential to detect process upsets more efficiently, and to identify and correct the source of the problem before system failure occurs.