Anaerobic membrane bioreactors (AnMBRs) offer an attractive option for treating industrial wastewaters under extreme conditions that might hamper granulation, biomass retention and reduce biological activity. This study assesses the long-term performance of an upflow anaerobic sludge blanket reactor (UASB) and an AnMBR treating highly saline phenolic wastewater. Analysis of bioreactor conversion, biomass characteristics and microbial community dynamics under increasing sodium and phenol concentrations is presented. The results demonstrated that compared to the UASB, the AnMBR process exhibited higher stability, likely due to its enhanced biomass retention. The AnMBR retained specialized microorganisms under increasing influent concentrations of phenol up to 5 gPh·L−1 and salinity up to 26 gNa+·L−1. In contrast, when the UASB reached this high influent phenol and high sodium concentration, deflocculation of biomass, apparently due to calcium leaching, was observed leading to a severe conversion capacity loss. Microbial community dynamics showed higher species evenness in the AnMBR compared to the UASB, leading to a higher methanogenic ability to respond to disturbances such as high phenol and sodium concentration increases. These findings highlighted the promising features of AnMBR technology, in widening the application potentials of high-rate anaerobic wastewater treatment and overcoming specific challenges in the treatment of chemical wastewater streams under extreme environmental conditions such as high salinity.