The performance of microbial fuel cells (MFCs) is limited by a number of factors, including metabolic activity of electroactive microorganisms and electrochemical systematic constraints, such as overpotentials at the electrodes or IR losses. Heterogeneities of substrate distribution (availability) can also strongly limit current in MFCs. In this work we investigate how mass transport can be enhanced by changing the flow configurations in MFCs, e.g. by directing the flow through a porous anode or by applying inserts and channels to anodes. Experimental results using a perpendicular flow through the anode were compared to a parallel flow setup, showing increased current output. Finite element method (FEM) simulations were used to simulate the flow profiles and substrate distribution in each setup. The simulations revealed higher average substrate concentrations for the perpendicular flow through a porous carbon fabric anode vs. a parallel flow in the bulk phase of the MFC, related to the enhancement of transport via convection in perpendicular flow. The simulated substrate distributions found for the different inlet setups could be correlated to the experimentally obtained current flow, power output and biofilm distribution. It can be concluded that the increased current output can be explained by the flow profile in the system resulting in an increased substrate distribution in the biofilm on the electrode and a hindered oxygen transport from the cathode.