This study was focused on the anaerobic digestion of residual biomass from the production of penicillin and l-cystine. The biogas potential tests of individual substrates and their mixture showed good anaerobic biodegradability. The highest measured specific biogas production was 712 l/kg volatile solids (VS) for penicillin biomass and 676 l/ kg VS for cystine biomass. The biogas potential tests were performed at different inoculum-to-substrate ratios (ISR) and showed that high concentrations of nitrogen and sulphur present in residual biomass have a major impact on the anaerobic processes. The long-term operation of the laboratory anaerobic reactor showed that the mono-digestion of the penicillin biomass was stable at an OLR of 1 kg/(m3.d). When co-digestion of penicillin and cystine biomass at a ratio of 0.9:0.1 (on a VS basis) and at the same OLR was enhanced, the operation of the laboratory model turned unstable. During this phase of the operation, the course of anaerobic processes was affected by ammonia and especially sulphide inhibition. Sulphide inhibition was effectively reduced by direct dosing of FeCl2 (in-situ sulphide control), at a molar iron-to-sulphur ratio of β = 1 (mol Fe/mol S). When suppressing sulphide inhibition, the operation of the laboratory model became stable even at a co-digestion ratio of 0.5:0.5 (VS basis). The results of this work open a new scope for future applications in the anaerobic digestion of waste biomass with high sulfur content, coming from industrial fermentation processes.