Covering the natural fibers with metal oxides enhances the antibacterial properties of textiles. The efficiency of the nanostructured layer is determined by its thickness, uniformity, configuration and adherence to the flexible substrate. Conformal coatings with ZnO and Al2O3 of cotton and viscose fabrics were achieved by Atomic Layer Deposition (ALD) at low temperature. Morphological examination conducted by Scanning Electron Microscopy (SEM) displayed the surface functionalization, elemental mapping provided by Energy Dispersive X-ray Spectroscopy (EDS) illustrated the uniform distribution of Zn and Al oxides, and the chemical structure stability was demonstrated by Fourier Transform Infrared Spectrometry (FTIR). The inhibition of Escherichia coli and Staphylococcus aureus evaluated after 18 h of incubation disclosed very good antibacterial properties of the organic-inorganic composites, with emphasis on viscose coated with metal oxides. In vitro cytotoxic studies developed through direct and indirect contact methods, highlighted the non-toxic effects of Al2O3 on human fibroblasts and keratinocytes.