This study investigated the impact of reverse salt flux (RSF) on microbe community and bio-methane production in a simulated fertilizer driven FO-AnMBR system using KCl, KNO3 and KH2PO4 as draw solutes. Results showed that KH2PO4 exhibited the lowest RSF in terms of molar concentration 19.1 mM/(m2.h), while for KCl and KNO3 it was 32.2 and 120.8 mM/(m2.h), respectively. Interestingly, bio-methane production displayed an opposite order with KH2PO4, followed by KCl and KNO3. Pyrosequencing results revealed the presence of different bacterial communities among the tested fertilizers. Bacterial community of sludge exposed to KH2PO4 was very similar to that of DI-water and KCl. However, results with KNO3 were different since the denitrifying bacteria were found to have a higher percentage than the sludge with other fertilizers. This study demonstrated that RSF has a negative effect on bio-methane production, probably by influencing the sludge bacterial community via environment modification.