BACKGROUND Two laboratory‐scale experimental systems – a membrane bioreactor (MBR) and a moving bed biofilm reactor–membrane bioreactor (MBBR‐MBR), both treating real high‐strength, saline wastewater from a table olive processing plant – were operated under identical conditions to comparatively evaluate their performance for three different hydraulic retention times (HRTs) of 88, 96 and 104 h. RESULTS The biological process of both systems, after appropriate biomass acclimatization, was stable and the removal efficiencies were rather high; i.e., regarding total organic carbon (TOC) ≥86.4% and ≥85.6% for the MBR and MBBR‐MBR, respectively, and ≥89.1% regarding total polyphenols (TPh) for both systems. Concerning TOC and TPh removal, no statistically significant difference (p < 0.05) was observed between the two systems. Reduction of HRT resulted in a slight decrease in mean TOC removal efficiency, but the mean TPh removal was practically unchanged. No membrane chemical cleaning was applied to either system during the 85‐day long continuous operation. CONCLUSION The comparative assessment showed that both systems (i.e., MBR and MBBR‐MBR) are effective for the advanced biological treatment of table olive processing wastewater and can achieve quite high removal efficiencies of organic matter and TPh. However, direct effluent reuse for irrigation purposes seems to be hindered by its high salinity. No significant differences were observed in the performance of these systems, apart from the increased aeration (and related energy costs), which is necessary to keep the biofilm carriers floating in the case of the MBBR‐MBR. © 2020 Society of Chemical Industry