In bioelectrochemical systems (BES), biofilm formation and architecture are of crucial importance, especially for flow-through applications. The interface between electroactive microorganisms and the electrode surface plays an important and often limiting role, as the available surface area influences current generation, especially for poor biofilm forming organisms. To overcome the limitation of the available electrode surface, nanoparticles (NPs) with a magnetic iron core and a conductive, hydrophobic carbon shell were used as building blocks to form conductive, magnetic micropillars on the anode surface. The formation of this dynamic three-dimensional electrode architecture was monitored and quantified in situ using optical coherence tomography (OCT) in conjunction with microfluidic BES systems. By cyclic voltammetry the assembled three-dimensional anode extensions were found to be electrically conductive and increased the available electroactive surface area. The NPs were used as controllable carriers for the electroactive model organisms Shewanella oneidensis and Geobacter sulfurreducens, resulting in a 5-fold increase in steady-state current density for S. oneidensis, which could be increased 22-fold when combined with Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) aggregates. In the case of G. sulfurreducens, the steady-state current density was not increased, but was achieved four times faster. The study presents a controllable, scalable and easy-to-use method to increase the electrode surface area in existing BES by applying a magnetic field and adding conductive magnetic NPs. These findings can most likely also be transferred to other electroactive microorganisms.