The work is aimed at elucidation of metabolite profile of probiotic yoghurts prepared from cow milk (CPY) and goat milk (GPY) using gas chromatography–mass spectrometry‐based untargeted metabolomics approach. A total of 192 metabolites including 49 differentially expressed metabolites (DEMs) were observed, wherein amino‐acids, peptides and analogues constituted 41.93% of the metabolite sub‐class. Acetic acid, glycine, Thr‐Ala, octanoic acid, l‐kynurenine and 2‐amino adipic acid were among the top 15 DEMs. A significant relationship with seven key metabolic pathways including glycolysis, lysine degradation, purine metabolism, fatty acid biosynthesis, tryptophan metabolism, nicotinate and nicotinamide metabolism and glycine, serine and threonine metabolism has been established based on their impact values.