Abstract Previous studies have confirmed significant removal of various trace organic contaminants (TrOCs) by white-rot fungal cultures under sterile batch test conditions. However, little is known about TrOC removal in continuous flow fungal reactors in a non-sterile environment. This study reports the removal of two TrOCs, namely, bisphenol A and diclofenac, by a fungal membrane bioreactor (MBR). Sterile batch tests with “active” (biosorption and biodegradation) and “chemically inactivated” (biosorption only) Trametes versicolor (ATCC 7731) confirmed biodegradation as the main mechanism for the removal of both compounds. An MBR inoculated with T. versicolor was operated in non-sterile conditions for a period of three months during which diclofenac and bisphenol A were continuously added to the synthetic wastewater. Relatively stable removal of bisphenol A (80–90%) and diclofenac (∼55%) was achieved by applying a hydraulic retention time of two days, at the bisphenol A and diclofenac loadings of 475 ± 25 and 345 ± 112 μg/L.d, respectively.