Relative change in the electrogenic activity and potential losses during electron transfer in microbial fuel cell (MFC) was elucidated using real-field recalcitrant pharmaceutical wastewater as anolyte by varying substrate/organic load (OL1, 1.98; OL2, 3.96; OL3, 5.93, OL4, 7.98 kg COD/m3). Increase in organic load showed improvement in electrogenic activity (OL4: 346 mV, 205.61 mW/m2; OL3: 320 mV, 158.58 mW/m2; OL2: 290 mV, 112.87 mW/m2; OL1: 256 mV, 72.60 mW/m2). Both activation and ohmic losses showed decrement with increase in organic load while concentration losses depicted increment. Improvement in power output was non-linear with increase in organic load due to the anodic over potentials, described as electron transfer resistances and potential losses. Bio-electrochemical analysis also depicted the electron losses in terms of electron discharge and energy generation with the function of varying organic load. © 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights.