Membrane contactors offer a promising feasible alternative to conventional desorption units due to their higher surface-to-volume ratio and operational flexibility. In this regard, a hollow fibre membrane contactor (HFMC) was coupled to a biogas desulphurisation reactor at pilot scale to recover the dissolved CH4 (D-CH4) present in the liquid effluent. To determine the effects of the operational parameters in the separation efficiency, different liquid (QL = 0.7–3 L min−1) and sweep gas flow rates (QG = 0.05–1 L min−1) were tested using a polypropylene HFMC. The D-CH4 removal efficiency (RE) was strongly dependent on the QL with a negligible effect of the QG, since the liquid phase boundary layer governed the mass transport. Thus, REs up to 70 % were obtained at QL ≤ 1 L min−1 feeding the liquid through the shell side. On the contrary, the CH4 content in the recovered gas was always quite low (<20 %) due to the sweep gas dilution effect and the simultaneous desorption of CO2. In log-term operation, a considerable loss of efficiency was observed when fouling appeared, therefore, different physical and chemical cleaning strategies were investigated. The permanent decline in the RE suggested a significant amount of irreversible fouling which hindered the cleaning efficiency, denoting the need of preventive cleanings. The analysis of the fibre surface elucidated an organic dense fouling cake, biofouling from bacteria and algae, and anhydrite scaling (CaSO4). Importantly, this study demonstrated that this process is an attractive prospect to avoid diffuse emissions and recover an energy vector.