This research sought to enhance the efficiency and biocompatibility of anodes in bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs), with an aim toward large-scale, real-world applications. The study focused on the effects of acid-heat treatment and chemical modification of three-dimensional porous pristine carbon felt (CF) on power generation. Different treatments were applied to the pristine CF, including coating with carbon nanofibers (CNFs) dispersed using dodecylbenzene sulfonate (SDBS) surfactant and biopolymer chitosan (CS). These processes were expected to improve the hydrophilicity, reduce the internal resistance, and increase the electrochemically active surface area of CF anodes. A high-resolution scanning electron microscopy (HR-SEM) analysis confirmed successful CNF coating. An electrochemical analysis showed improved conductivity and charge transfer toward [Fe(CN)6]3−/4− redox probe with treated anodes. When used in an air cathode single-chamber MFC system, the untreated CF facilitated quicker electroactive biofilm growth and reached a maximum power output density of 3.4 W m−2, with an open-circuit potential of 550 mV. Despite a reduction in charge transfer resistance (Rct) with the treated CF anodes, the power densities remained unchanged. These results suggest that untreated CF anodes could be most promising for enhancing power output in BESs, offering a cost-effective solution for large-scale MFC applications.