Metabolic syndrome is characterized by several cardio-metabolic risk factors including obesity, hypertension, insulin resistance, and is related to the risk of developing type 2 diabetes (T2D). The discovery of new molecules, which can be used as safe alternative to drugs and improve the glucose metabolism, will reduce the incidence of T2D. The aim of the study was to test the ability of alpine cheese-resident lactic acid bacteria to produce health-promoting metabolites, such as gamma-aminobutyric acid (GABA) and conjugated linoleic acids (CLA). Lactobacillus brevis FEM 1874, previously reported as GABA producer strain, was tested in vivo on mice suffering obesity and T2D. Lb. brevis FEM 1874 survived gastro-intestinal digestion and showed some physiological effect into the animals. This study demonstrates that microbiota from traditional mountain products harbors great health-promoting properties and is able to produce bioactive metabolites. This would contribute to the development of new multifunctional foods, enriched with bio-functional molecules.