Effective control of anaerobic digestion in biogas plants requires the monitoring of process sensitive and rapid response parameters in order to ensure efficient biogas production and to prevent potential process failure. In this study, stable carbon isotopes of methane (δ13CCH4) produced in a full-scale continuous stirred-tank reactor were investigated as a potential new monitoring tool for this purpose. Over a six-month period with variable organic loading rates, δ13CCH4-values were measured online by a portable high-precision laser absorption spectrometer. During a stress period of consecutive high organic loading, δ13CCH4-values early indicated process changes in contrast to traditionally monitored parameters where a change was observed some five to ten days later. Comparison of the stable isotope values with data from microbial analyses showed a distinct relationship between the quantity of potentially acetoclastic methanogens and δ13CCH4-values. This finding indicates an association between dominant methanogenic pathways and carbon isotope values.