Abiotic stress has major impacts on crop yields worldwide. In the field, multiple stresses often occur simultaneously, and interactions between these stresses will modify the physiological response of plants. We briefly review known tolerance mechanisms and describe approaches that led to their identification, and how new tolerance mechanisms may be identified using ‘omics technologies. We then focus on metabolomics technologies including data analysis, and the results of their application in abiotic stress research. Integration of multiple ‘omics datasets and their interpretation with existing genetic, physiological and morphological data is a challenge that is currently being addressed to enable further exploration and interpretation of metabolomic data. We conclude by discussing new developments in metabolomics, such as single cell measurements of stress responses and tissue-based mass spectrometry imaging that will offer greater spatial resolution of sub-cellular distribution of metabolites.