The low-efficiency rate of urban wastewater (UWW) treatment generates tons of discharged water with a high concentration of pollutants, pathogens and antibiotic-resistance genes (ARGs). Microalgal systems may be a green alternative to be implemented as a UWW polishing treatment. This study assessed the ability of Chlorella vulgaris and UWW autochthonous microalgal species (AMS) to simultaneously remove PO4–P, and reduce the proliferation of coliforms and ARGs. AMS seems to be more promising due to: (i) the higher specific growth rate, μmax (0.687 ± 0.065 d−1); (ii) efficient PO4–P removal (92.62 ± 0.10%); (iii) faster reduction of coliforms proliferation achieving concentrations below the limits of quantification (6 d); (iv) the reduction of intl1 and the ARGs sul1 and blaTEM abundance in ca. of 70.4%, 69.2%, and 75.7%, respectively (9 d); and (v) the additional reduction of these genes in ca. of 97.1%, 94.2%, and 99.9%, respectively, after 5 d storage in the dark and at room temperature. Results also revealed that the high pH values in both microalgal systems (due to microalgal growth) were highly correlated with a reduction in the proliferation of coliforms, including Escherichia coli. In conclusion, using AMS as a final polishing treatment of UWW seems to be very promising.