•A biotrickling filter was installed and operated at pilot-scale in a WWTP in Spain.•Operating conditions for biogas desulphurisation at acidic environment were determined.•An average elimination capacity of 169gH2Sm−3h−1 was obtained on the long-term.•Partial oxidation to elemental sulphur was envisaged to be the preferred mechanism.•Acidithiobacillus thiooxidans was dominant on the microbial consortium. The most harmful biogas contaminant for energy conversion equipment such as fuel cells is hydrogen sulphide (H2S); thus efficient and cost-effective treatment systems for this compound should be designed and developed. A pilot-scale biotrickling filter (BTF) working in acidic media (pH=1.5–2) was operated for raw sewage biogas desulphurisation. Its operational performance as a function of two key important process parameters (temperature and retention time) was evaluated through short-term experimentation; showing that H2S removal efficiencies greater than 90% can be obtained at temperatures of 30°C, retention times of 80–85s and H2S Loading Rates of 210gH2S/(m3bedh). The system was afterwards operated for 924h and showed an average elimination capacity of 169gH2S/(m3bedh) at an average removal efficiency of 84%. The unit proved to be reversible to the effect of operation disruptions (lack of temperature control, limitations on oxygen supply), which were introduced to simulate possible system miss functioning or operational failures. Nevertheless, partial oxidation to elemental sulphur (S(s)) accounted for 70% of H2S removal progressively increasing the pressure drop over the column; reducing the availability of the treatment line and eventually leading to fuel cell shutdowns. More efficient systems for oxygen supply and solids removal are the key factors to be addressed for a sustainable deployment of BTF technology in waste water treatment plants (WWTP).