Rapid acidification and inhibition by d-limonene are major challenges of biogas production from citrus waste. As limonene is a hydrophobic chemical, this challenge was encountered using hydrophilic polyvinylidine difluoride (PVDF) membranes in a biogas reactor. The more sensitive methane-producing archaea were encapsulated in the membranes, while freely suspended digesting bacteria were present in the culture as well. In this membrane bioreactor (MBR), the free digesting bacteria digested the citrus wastes and produced soluble compounds, which could pass through the membrane and converted to biogas by the encapsulated cell. As a control experiment, similar digestions were carried out in bioreactors containing the identical amount of just free cells. The experiments were carried out in thermophilic conditions at 55 °C, and hydraulic retention time of 30 days. The organic loading rate (OLR) was started with 0.3 kg VS/m3
/day and gradually increased to 3 kg VS/m3
/day. The results show that at the highest OLR, MBR was successful to produce methane at 0.33 Nm3
/kg VS, while the traditional free cell reactor reduced its methane production to 0.05 Nm3
/kg VS. Approximately 73% of the theoretical methane yield was achieved using the membrane bioreactor.