The objective of this work was to determine by metagenomics the effect of advanced oxidation systems on the taxonomic and functional diversity of pathogenic microorganisms in the effluent of the Salitre wastewater treatment plant in Bogotá (Colombia). The taxonomic and functional diversity of the microorganisms before and after treatment was determined by Illumina mass sequencing, human pathogenic genera detecting as Pseudomonas (28.0%), Arcobacter (10.0%), Aeromonas (4.0%), Sulfurospirillum (4.0%), Salmonella (3.0%), and Clostridiales (3.0%). Likewise, pathogenicity factors such as antimicrobial resistance genes (ARGs) also were detected in high abundances (~5% of metagenome reads). The effluent was treated by photoelectro-Fenton system for five-minute, obtaining a significant reduction of pathogenicity factors (near-zero logs2 values) such as ARGs, chemotaxis, DNA repair, quorum sensing, secretion systems, and toxins of pathogenic bacteria such as Arcobacter, Pseudomonas, Serratia, and Salmonella. Hence, the photo-electro-Fenton process showed to be a promising alternative to deal with municipal effluents removing pathogenicity factors such as ARG, chemotaxis, DNA repair, quorum detection, secretion systems, and toxins of pathogenic bacteria.