In this work, the occurrences of bacteria families and relevant pharmaceuticals in municipal wastewater effluents from Bogotá (Colombia), and their treatment by the photo-electro-Fenton process were studied. Twenty-five representative pharmaceuticals (azithromycin, carbamazepine, ciprofloxacin, clarithromycin, diclofenac, enalapril, gabapentin, iopromide, metoprolol, sulfamethoxazole, trimethoprim, valsartan, clindamycin, erythromycin, levamisole, lincomycin, norfloxacin, oxolinic acid, phenazone, primidone, salbutamol, sulfadiazine, tetracycline, tramadol, and venlafaxine) were quantified in the effluent by LC-MS/MS analysis. Four of these target compounds (azithromycin, diclofenac, trimethoprim, norfloxacin) were found at concentrations that represent an environmental risk. In addition, several bacteria families related to water and foodborne diseases were identified in such effluents (e.g., Pseudomonadaceae, Campylobacteraceae, Aeromonadaceae, Enterobacteriaceae, and Bacteroidaceae), via shotgun-metagenomic technique. Then, a bench-scale photo-electro-Fenton (PEF) system equipped with a DSA anode (Ti/IrO2-SnO2) and a GDE cathode was applied to treat such effluents. After 60 min, this treatment led to a decrease in the ratio of the bacterial content in the original samples, ~150 thousand times, and a pondered removal of 66.12% for the pharmaceuticals. The study of the process pathways indicated that the bacteria and pharmaceuticals elimination mainly occurred through attacks of hydroxyl and chlorine radicals. Interestingly, in the case of pharmaceuticals, their environmental risk quotients were diminished after the PEF application. Furthermore, the prolonged action of this electrochemical process induced ~15% of mineralization and a significant reduction of the total DNA (removal >85%). Hence, the photo-electro-Fenton process showed to be a promising alternative to deal with municipal effluents for limiting the waterborne diseases, pollution by pharmaceuticals, and mobility/availability of genetic material coming from microorganisms.