This dataset contains experimental data on the on the biological, physical and biochemical characterization of Lactobacillus delbrueckii subsp. bulgaricus CFL1 in the presence of three protective formulations: a galacto-oligosaccharides-contining extract from chickpeas cooking wastewater (GOS), produced in the frame of PREMIUM project (777657) (Martins et al 2023), a commercial fructo-oligosaccharides product from inulin (FOS), and sucrose, and at different steps of the stabilization process (freezing, freeze-drying and two weeks of storage at 28°C). The data set includes i) biological activity (culturability, acidifying activity, viability), ii) physical properties of the matrix (glass transition temperature and water content), iii) biochemical composition (Fourier transform infrared features), iv) biophysical (membrane integrity and phospholipid organization) and fermentation data (optical density and acidification rate as a function of time).