The ligninolytic enzymes versatile peroxidase (VP) and manganese peroxidase (MnP) have been previously described as efficient oxidizers of the endocrine disrupting chemical (EDC) nonylphenol at high concentrations of the pollutant. Envisaging the application of an enzymatic technology as a tertiary treatment in wastewater treatment plants, it is important to design a continuous reactor that performs the efficient removal of nonylphenol under environmental conditions. In the present research, a two-stage membrane bioreactor based on the production and use of Mn3+-malonate (chemical oxidant) was applied. The bioreactor consisted of an enzymatic reactor (R1) for the production of Mn3+-malonate by VP, coupled to an oxidation reactor (R2), where the oxidation of nonylphenol by Mn3+-malonate took place. The production of Mn3+-malonate in R1 was maintained constant: 500–700 μM with minimal deactivation of the enzyme. The oxidation reactor attained nearly complete removal of nonylphenol, even at a hydraulic retention time (HRT) shorter than 20 min. The operation with real wastewater containing nonylphenol at environmental concentrations (454 nM) was also successful, with a nonylphenol removal of 99.5 % at a rate of 0.73 μM h−1. Moreover, when the HRT of R2 was sharply reduced to 6.8 and 3.6 min, the removal of nonylphenol was maintained beyond 99 %, which proves the feasibility of the system to remove the target compound present in a real effluent, even at very short HRTs.