Chickpeas and lentils contain prebiotic carbohydrates, including galacto-oligosaccharides (GOS), that confer health benefits but can also lead to undesirable effects like bloating and flatulence. Legume processing reduces these disadvantages and usually consists of the soaking and cooking of the legume seeds. In their industrial production, the processing water is considered waste. As different carbohydrates have recognized stabilization properties on lactic acid bacteria during dehydration processes, this study aimed to investigate the protective effect of GOS-containing wastewater extracts from cooking chickpeas and lentils, as well as fructo-oligosaccharides, and sucrose (used for comparative purposes), on the stability of freeze-dried Lactiplantibacillus plantarum WCFS1, by measuring biological (culturability, storage stability, acidifying activity), chemical (pH), and physical (water content) properties. The best storage stability was observed for mixtures with GOS-containing wastewater legume extracts. Protection of lactic acid bacteria strains with GOS-containing wastewater legume extracts would limit their spoilage in food production, positively impacting the environment.