The influence of Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB12 in cofermentation with traditional starters on metabolite formation in set yoghurt was evaluated. Microbial activity during fermentation and refrigerated storage was investigated by monitoring bacterial population dynamics, milk acidification and overall changes in yoghurt metabolite profiles. A complementary metabolomics approach using solid-phase microextraction-gas chromatography/mass spectrometry and 1H nuclear magnetic resonance resulted in the identification of 37 volatile and 43 non-volatile metabolites, respectively. Results demonstrated that the two probiotic strains did not influence acidity and the key-aroma volatile metabolites of set yoghurt. However, a contribution by the presence of L. rhamnosus GG on the non-volatile metabolite profile of yoghurt was specifically noticed during storage. Multivariate analysis allowed yoghurts fermented by different starter combinations and different durations of storage to be differentiated according to their metabolite profiles. This provides new insights regarding the impact of probiotics on the metabolome of yoghurt.