Enrichment of yoghurts with additional bacterial strains holds the potential to improve the nutritional value of the product. By incorporating an adjunct strain in combination with the starter culture, 183 enriched yogurts were produced, covering 19 species from 9 different genera. Interestingly, this enrichment substantially increased the total number of metabolites produced. Moreover, the set of newly produced metabolites alone was sufficient for a clear cluster-separation of yoghurts enriched with adjunct strains from the same genus. Furthermore, 35 metabolites known to be aroma compounds or associated with beneficial health effects were identified by targeted metabolomics. Determination of the relative concentration of these metabolites revealed that a set of enriched yoghurts produced high concentrations of DL-indole-3-lactic acid, 3-phenyllactic acid, short-chain fatty acids, amino acids and the neurotransmitter gamma-aminobutyric acid, particularly in yoghurts enriched with Lactobacillus, Propionibacterium, or Acidipropionibacterium strains, having the potential to further improve the health benefits associated with consumption of yoghurt. This study is the first in which a comprehensive series of enriched yoghurts were produced by adding an adjunct strain, followed by a metabolic profiling using three different platforms (LC-MS, GC-MS, and GC-MS volatiles), allowing the identification of a wide variety of different compounds.