This paper is focused on the experimental implementation of a robust control scheme for the regulation of volatile fatty acids (VFA) in continuous anaerobic digestion processes. The robust scheme is made of an output feedback control, and an extended Luenberger observer is used to estimate the uncertain terms of the process (i.e.. influent concentration and process kinetics). The control scheme is implemented in a pilot plant up-flow fixed-bed reactor that is treating industrial wine distillery wastewater. The performance of the robust scheme is tested over a period of 36 days, under different set-point values and several uncertain scenarios, including model mismatch, badly known parameters, and load disturbances. Experimental results show that the VFA concentration can be effectively regulated over a wide range of operating conditions. In addition, it is shown that the control scheme has a structure that improves its performance in the presence of noisy measurements and control input saturations.