Oligosaccharides, well-known for their prebiotic properties, are reported as promising protective carbohydrates for ensuring the long-term stability of dried lactic acid bacteria and probiotics. This study examines the mechanisms involved in the freeze-drying and storage protective abilities of an extract from chickpea’s cooking wastewater containing galacto-oligosaccharides, a fructo-oligosaccharide inulin-derived product, and sucrose on Lactobacillus delbrueckii subsp. bulgaricus CFL1, a strain highly sensitive to stabilization steps. Fourier transform infrared microspectroscopy analysis demonstrated significant molecular changes in cell components after freeze-drying regardless of the protectant used. The freeze-drying led to damage to proteins, peptidoglycans of the cell wall, nucleic acids, and induced membrane integrity losses. The highest resistance to freeze-drying observed with the galacto-oligosaccharides extract was associated with its ability to immobilize cells in a glassy matrix, presenting a glass transition temperature well above the desorption temperature, and its interaction with the phospholipids of the bacterial membrane.