Anodes modified with MnO2, Pd and Fe3O4 nanoparticles were used in microbial fuel cells (MFCs) and their effects on pharmaceutically active compounds (PhACs) removal and power generation were investigated. Results showed that anode decoration with MnO2, Fe3O4 and Pd led to different performance in removing PhACs from MFCs. Diclofenac (DCF), ibuprofen (IBF) and carbamazepine (CBZ) were more effectively removed in the MFCs with the MnO2, Fe3O4 or Pd anode compared to that with the carbon black (CB) modified control anode, with a removal of 81.5%-84.0% for CBZ, 48.7%-52.6% for DCF and 18.8%-20.1% for IBF, while the corresponding parts attained with the CB anode were 71.0%-78.5% for CBZ, 28.8% for DCF and 14.6% for IBF. Iohexol (IOX) was hardly removed in all the MFCs. When common non-conductive carrier (nonwoven) was used as the anode of MFCs, PhACs were less removed compared to the MFC systems, suggesting MFCs possess specially advantages over PhACs removal. The MFCs with the Pd, MnO2 and Fe3O4 anodes generated a maximum power density of 824 +/- 36, 782 +/- 37 and 728 +/- 33 mWm(-2), respectively, higher than that with the control anode (680 +/- 28 mWm(-2)). High-throughput sequencing results showed that the MnO2 and Fe3O4 modified anodes especially enriched the exoelectrogen Geobacter (72.1%), while the Pd decorated anode enriched a high abundance of Geobacter (38.5%) and Sphaerochaeta (16.1%). Enhanced electron transfer, specially enriched microbial community, unique catalytic functions of the metal or metal oxides deposited on the anodes, may contribute to the enhanced performance of MFCs on power generation and PhACs removal.