This work evaluated the electrochemical, physical, biochemical, and molecular characterization of electrogens from a graphite felt anode when zinc oxide on activated carbon (ZnO/AC) was used as a cathodic electrocatalyst in a double-chambered microbial fuel cell (DCMFC). The electrochemical polarization behavior of the DCMFC showed that ZnO/AC had a higher power density (PDmax) of 89 mW m−2 with a corresponding cell current density (CD) of 248 mA m−2 and a voltage output of 395 mV, which was higher than those of the blank electrode used as a benchmark (PDmax of 68 mW m−2 at a CD of 161 mA m−2 and a voltage of 421 mV). Furthermore, scanning electron microscopy and transmission electron microscopy revealed that the morphology and interior properties of the strains varied among the rods (bacilli), spirals (vibrios), and spheres (diplococci, staphylococci and streptococci). In addition, biochemical characterization via the Vitek2 compact system and molecular analysis via 16 S rRNA and 18 S rRNA gene sequencing revealed the occurrence of nine prevalent species that were correlated with Sphingobacterium spiritivorum, Ochrobactrum anthropicus, Pseudomonas mendocina, Stenotrophomonas maltophilia, Leuconostoc mesenteroides, Staphylococcus equorum, Bacillus subtilis HQ334981.1, Kocuria kristinae KC581674.1 and Saccharomyces cerevisiae NR111007.1. Consequently, the present study outlines different characterization strategies for electrogenic microbes that play an important role in the overall performance of DCMFC for scaling up and managing existing environmental pollution for sustainable energy generation.