This data set concerns the physico-chemical, biological and biochemical characterization of two lactic acid bacteria. The objective was to assess their different resistance to drying and describe the degradation mechanisms related to freeze- and spray-drying. Lactobacillus delbrueckii ssp bulgaricus CFL1 and Lactiplantibacillus plantarum WCFS1 were investigated. The dataset contains, for each strain, the results for the following studies: i) biological activity: culturability and acidifying activity; ii) flow cytometry: viable, dead and injured cells; iii) physico-chemical properties: water activity and glass transition temperature of dried samples; and iv) biochemical characterization by Fourier transform infrared microscopy of cells in an aqueous environment. These measurements were performed after freezing, after freeze- and spray-drying, and after 28 days of storage at 4, 23 and 37 °C. The glass transition temperature of the frozen samples was also measured.