Anode properties are critical for the performance of microbial electrolysis cells (MECs). In the present study, Fe nanoparticle-modified graphite disks were used as anodes to investigate the effects of nanoparticles on the performance of Shewanella oneidensis MR-1 in MECs. Results demonstrated that the average current densities produced with Fe nanoparticle-decorated anodes up to 5.89-fold higher than plain graphite anodes. Whole genome microarray analysis of the gene expression showed that genes encoding biofilm formation were significantly up-regulated as a response to nanoparticle-decorated anodes. Increased expression of genes related to nanowires, flavins, and c-type cytochromes indicates that enhanced mechanisms of electron transfer to the anode may also have contributed to the observed increases in current density. The majority of the remaining differentially expressed genes associated with electron transport and anaerobic metabolism demonstrate a systemic response to increased power loads.