This study investigated the surface and electrochemical properties of carbon cloth electrodes surface-modified by using atmospheric pressure plasma jets (APPJs) for applications involving microbial fuel cells (MFCs). APPJ treatment made the carbon cloth highly hydrophilic and did not introduce any observable cracks or flaws. MFCs configured with APPJ-treated carbon cloth electrodes exhibited electrochemical performance (maximum power density of 7.56 mW m−2) superior to that of MFCs configured with untreated carbon cloth electrodes (maximum power density of 2.38 mW m−2). This boost in performance can be attributed to the formation of abundant carboxyl and ammonium functional groups on the surface of APPJ-treated carbon cloth, which promoted the formation of anodic biofilms and the adhesion of bacteria, while facilitating the transfer of electrons from the bacteria to the electrodes. APPJ surface modification is non-toxic and environmentally friendly (no exogenous chemicals are required), which is particularly beneficial as the introduction of toxins might otherwise inhibit bacterial growth and metabolism. The APPJ surface modification process is rapid, cost-effective, and applicable to substrates covering a large area, making it ideal for the fabrication of large-scale MFCs and bioelectrochemical bioenergy devices.