A pilot-scale biotrickling filter (BTF) was operated in counter-current flow mode under anoxic conditions, using diluted agricultural digestate as inoculum and as the recirculation medium for the nutrient source. The process was tested on-site at an agricultural fermentation plant, where real biogas was used. The pilot plant was therefore exposed to real process-related fluctuations. The purpose of this research was to attest the validity of the filtration process for use at an industrial-scale by operating the pilot plant under realistic conditions. Neither the use of agricultural digestate as trickling liquid and nor a BTF of this scale have previously been reported in the literature. The pilot plant was operated for 149 days. The highest inlet load was 8.5 gS-H2Sm-3h-1 with a corresponding removal efficiency of 99.2%. The pH remained between 7.5 and 4.6 without any regulation throughout the complete experimental phase. The analysis of the microbial community showed that both anaerobic and anoxic bacteria can adapt to the fluctuating operating conditions and coexist simultaneously, thus contributing to the robustness of the process. The operation of an anoxic BTF with agricultural digestate as the trickling liquid proved to be viable for industrial-scale use.