Anode modification with MnO2, Pd and Fe3O4 nanoparticles was evaluated for pharmaceutically active compounds (PhACs) removal and power generation in microbial fuel cells (MFCs). The MFCs with Pd, MnO2 and Fe3O4 anodes achieved a maximum power density of 824, 782 and 728 mW m-2, respectively, which were higher than that with carbon black (CB) modified anode (680 mW m-2) and nonwoven cloth (NW) anode (309 mW m-2). The removal percentages of carbamazepine and diclofenac in MFCs with MnO2, Pd and Fe3O4 anodes were more than 80% and 50%, respectively, while ibuprofen and iohexol showed limited biodegradation. MnO2 and Fe3O4 anodes possessed removal mechanisms of chemical oxidation or reduction and biodegradation. This work for the first time reported the anode modification with MnO2, Pd and Fe3O4to enhance PhACs removal and power generation, which may help to understand the role of metal and metal oxides nanoparticles in the degradation of PhACs and power generation in a bioelectrochemical system.