This dataset comprises experimental data on the biological, physical and biochemical characterization of Ligilactobacillus salivarius CECT5317 in the presence of different protective molecules (maltodextrin alone or in mixtures with fructooligosaccharides, trehalose, or antioxidants) and at different steps of the stabilization process (freezing, freeze-drying and accelerated storage). The dataset includes i) biological activity (culturability), ii) physical properties of the matrix: glass transition temperature and water activity, iii) membrane fatty acid composition and iv) biochemical composition by Fourier transform infrared microscopy of cells in an aqueous environment before and after freeze-thawing, after freeze-drying and during 4 weeks of storage at 37 °C.