Despite the prevalence of Saccharomyces yeasts in industrial fermentation , there is increasing interest in non-Saccharomyces yeasts, triggered by their rich and diverse reservoir of enzymes and secondary metabolites not typically produced by representative Saccharomyces yeasts (Fig. ). The metabolic diversity provided by non-Saccharomyces yeasts has promise for meeting consumer demands for new sensorial and beneficial health properties, but without the challenges of mixed microbial ferments. In concert, metabolomics technologies have provided essential data to measure and evaluate the molecular impact and potential of non-Saccharomyces yeasts and their metabolites in fermented beverages. This mini-review addresses recent developments in the use of metabolomics to study the use of non-Saccharomyces yeasts in the production of fermented beverages.