This study concerns the evaluation of the protective ability of oligosaccharides (FOS produced by enzymatic synthesis from sucrose) to preserve three lactic acid bacteria (Lactobacillus delbrueckii ssp bulgaricus CFL1, Lactobacillus plantarum WCFS1, and Carnobacterium maltaromaticum CNCM I-3298) during freezing, freeze-drying at pilot scale, and two weeks of storage of freeze-dried samples at 25°C. The dataset includes, for each of the three strains: i) the fermentation conditions (temperature, pH, and base consumption); ii) the stabilization conditions (freezing temperature and containers, freeze-drying recipe and parameters monitored during the cycle); iii) the quantification of the acidifying activity (using the CinAc system, AMS, Frepillon, France) and viability (using the plate count method) before and after freezing, after freeze-drying, and after storage.