This paper describes an automatic sampling system for anaerobic reactors that allows taking representative samples following the guidelines of Gy’s (1998) theory of sampling. Due to the high heterogeneity degree in a digester the sampling errors are larger than the analysis error, making representative sampling a prerequisite for successful process control. In our system, samples are automatically processed, generating a higher density of data and avoiding human error by sample manipulation. The combination of a representative sampling system with a commercial automate titration unit generates a robust online monitoring system for biogas plants. The system was successfully implemented in an operating biogas plant to control a feeding-on-demand biogas system.