Wastewater (WW) from urban and industrial activities is often contaminated with microorganisms and chemical pollutants. To reduce the concentration of microorganisms in WW to levels comparable to those found in natural waters, the sewage effluent is usually subjected to disinfection with chlorine, ozone, or ultraviolet light, which may lead to the formation of toxic products and contribute to the selection of resistant genes. Moreover, the changing patterns of infectious diseases and the emerging of multidrug resistant microbial strains entail the development of new technologies for WW decontamination. Microbial photodynamic inactivation (PDI) with photosensitizers, oxygen, and visible light has demonstrated to be effective in the inactivation of microorganisms via photogeneration of reactive oxygen species able to induce microbial damage at the external structures level. The promising results of PDI suggest that this principle can be applied to WW treatment to inactivate microorganisms but also to photodegrade chemical pollutants. The aim of this study was to assess the applicability of PDI for the microbial and chemical decontamination of secondarily treated WW. To evaluate the efficiency of bacterial inactivation in WW, experiments were done in both phosphate buffer saline (PBS) and filtered WW with the bioluminescent Escherichia coli, using small and large volumes of WW. The potential of PDI to inactivate the native bacteria (E. coli and Enterococcus) present in WW was tested and assays without the adding of bacteria to the WW were performed. It was also tested if the same PDI protocol was able to induce phototransformation of phenol. The cationic porphyrin 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetra-iodide (Tetra-Py + -Me) was shown to be effective against both bacterial groups representing both Gram-negative and Gram-positive bacteria used as microbiological parameters to instigate water quality and even showing the power to photooxidate organic compounds. As the photosensitizer when immobilized on solid matrixes can be easily removed, recovered, and reused, an effective, less-expensive, easy-applicable, and environmentally friendly technology can be applied to treat WW, inactivating microorganisms and degrading chemical contaminants at the same time.