Six pharmaceutical pastes were prepared using chemically modified kaolin and talc powders. Tests were conducted to determine their structural and chemical characteristics as well as their antimicrobial protection, thus rendering them suitable for cosmetic and pharmaceutical uses. Kaolin and talc were treated chemically via the cation exchange method to load the clay particles with copper and zinc ions, two cations well known for their antimicrobial properties. Mineralogical analyses were conducted by using X-ray diffraction (XRD) before and after the modification, confirming the mineralogical purity of the samples. Scanning electron microscopy was also used in conjunction with energy dispersed spectroscopy (SEM-EDS) to obtain chemical mapping images, revealing the dispersion of the added metals upon the clay minerals surfaces. Moreover, chemical analysis has been performed (XRF) to validate the enrichment of the clays with each metal utilizing the cation exchange capacity. All modified samples showed the expected elevated concentration in copper or zinc in comparison to their unmodified versions. From the X-ray photoelectron spectroscopy (XPS), the chemical state of the samples’ surfaces was investigated, revealing the presence of salt compounds and indicating the oxidation state of adsorbed metals. Finally, the resistance of pastes in microbial growth when challenged with bacteria, molds, and yeasts was assessed. The evaluation is based on the European Pharmacopeia (EP) criteria.