This research investigated the impact of permeate flux and gas sparging rate on membrane permeability, dissolved and colloidal organic matter (DCOM) rejection and process economics of granular anaerobic membrane bioreactors (AnMBRs). The goal of the study was to understand how membrane fouling control strategies influence granular AnMBR economics. To this end, short- and long-term filtration tests were performed under different permeate flux and specific gas demand (SGD) conditions. The results showed that flux and SGD conditions had a direct impact on membrane fouling. At normalised fluxes (J20) of 4.4 and 8.7 L m−2 h−1 (LMH) the most favourable SGD condition was 0.5 m3 m−2 h−1, whereas at J20 of 13.0 and 16.7 LMH the most favourable SGD condition was 1.0 m3 m−2 h−1. The flux and the SGD did not have a direct impact on DCOM rejection, with values ranging between 31 and 44%. The three-dimensional excitation-emission matrix fluorescence (3DEEM) spectra showed that protein-like fluorophores were predominant in mixed liquor and permeate samples (67–79%) and were retained by the membrane (39–50%). This suggests that protein-like fluorophores could be an important foulant for these systems. The economic analysis showed that operating the membranes at moderate fluxes (J20 = 7.8 LMH) and SGD (0.5 m3 m−2 h−1) could be the most favourable alternative. Finally, a sensitivity analysis illustrated that electricity and membrane cost were the most sensitive economic parameters, which highlights the importance of reducing SGD requirements and improving membrane permeability to reduce costs of granular AnMBRs.