Metabolomics is the scientific study of the unique chemical fingerprints that result from specific biochemical processes. It enables the comprehensive detection and quantification of small molecules that are intermediates or end-products of metabolism in a biological sample, such as a grape or yeast. The metabolomics approach also provides for a holistic characterisation of complex chemical transformations and oxidation reactions during winemaking, ageing and transport. The development of metabolomics has made major advances in the last two decades. Improved chromatographic techniques for separation of polar metabolites and enhanced sensitivity and selectivity of nuclear mass resonance and mass spectrometric instrumentation now enable detection and quantification of hundreds of metabolites in a single analysis. New bioinformatics tools and statistics capabilities are available which are key to efficiently analysing and annotating comprehensive datasets. This review provides an overview of analytical methods for untargeted profiling, biomarker discovery and targeted analysis of non-volatile and volatile metabolites. It summarises bioinformatics tools for data processing, data mining and metabolite identification and explores metabolomics approaches which have been successfully employed to comprehensively analyse, annotate and understand the broad chemical diversity in grapes, yeast and wine. It also describes opportunities for the application of metabolomics in grape and wine science and provides an outlook about further development needs and emerging trends.