Two series of antimicrobial polymethacrylates (PMTAs) bearing mono and bis-cationic quaternary ammonium cations (QUATs) were prepared by controlled N-alkylation of 1,3-thiazole and 1,2,3-triazole pendant groups with butyl iodide (PMTAs-BuI). The degree of quaternization (DQ) of the azole heterocycles was monitored by (1)H NMR spectroscopy over a wide range of reaction times. Spectra analysis of the (1)H NMR aromatic region allowed to characterize and quantify the different species involved and, therefore, to control the chemical composition distribution of the amphiphilic polycations. The polymer charge density and the hydrodynamic sizes were measured by zeta potential and dynamic light scattering (DLS), respectively. Consequently, the relationship between structure and antibacterial properties and toxicity was studied. Interestingly, these polyelectrolytes present excellent selective toxicity against bacteria being nonhemolytic even at low values of DQ. Furthermore, they were also evaluated for their microbial time-killing efficiency, presenting a 3 log-reduction in only 15 min. Additionally, the bacteria cell morphology treated with PMTAs-BuI was analyzed.