This dataset contains experimental data on an extensive characterization of bacterial cells obtained by two sets of production conditions providing two significantly different strain resistance to the manufacturing process (here called sensitive and resistant). We used such different cell concentrates for identifying markers of cell injury. L. salivarius CECT5713 concentrates produced under the two sets of production conditions were characterized using a multiscale (matrix, cell population, cell membrane and other cell components) and multistep (freezing, freeze-drying, storage) approach. Apart from the production conditions of cell concentrates (culture and protection), the dataset includes i) biological activity (culturability, viability, and storage stability), ii) physical properties of the matrix (glass transition temperature and water activity), iii) membrane properties (fatty acid composition, membrane fluidity, and phospholipid organization by measuring the lipid membrane phase transition), and iv) biochemical composition (Fourier transform infrared microscopy in aqueous environment-FTIR features) following freezing, freeze-drying, and 4 weeks of storage at 37°C.