Extreme environmental changes and fluctuations mainly driven by climate change will have a profound effect on natural food contaminants. Among these contaminants mycotoxins will be very important due the high adaptability of the producing fungal genera to the forecasted conditions. The availability of modern, high through-put –omic techniques, including genomics, transcriptomics, metagenomics, proteomics and metabolomics has facilitated a rapid expansion of data on the biology of mycotoxigenic fungi. This has facilitated a significant increase in our knowledge of the biological, biochemical and biophysical molecular processes regulating the production of mycotoxins, and the adaptation of these fungi to environmental stresses. In this paper we highlight recent advances where -omics approaches have been used and where they have contributed to the knowledge on how mycotoxigenic fungi adapt to diverse interacting environmental conditions and their relationship with phenotypic toxin production. We also highlight potential future directions where these approaches can be effectively utilised for the development of minimisation strategies in the context of expected climate change scenarios and the food security agenda.