Mycotoxins are toxic secondary metabolites of low molecular weight produced by filamentous fungi, such as Aspergillus, Fusarium, and Penicillium spp. The presence of mycotoxin in agricultural commodities is an inevitable consequence of production processes and may increase due to global environmental change. Dangerous mycotoxins cause a variety of health problems not only for humans but also for animals. Based on toxicity, they can be classified as carcinogens, immunosuppressive, hepatotoxins, nephrotoxins, and neurotoxins. Hence, various approaches have been used to assess and control mycotoxin contamination. Significant challenges still exist because of the complex heterogeneous nature of food composition. The potential of combined omics approaches such as metabolomics, genomics, transcriptomics and proteomics would contribute to our understanding about pathogen fungal crosstalk as well as strengthen our ability to identify, isolate and characterise mycotoxins pre- and post-harvest. Multi-omics approaches along with advanced analytical tools and chemometrics provide a complete annotation of such metabolites produced before/during the contamination of crops. We have assessed the merits of these individual and combined omics approaches and their promising applications to mitigate the issue of mycotoxin contamination. The data included in this review focus on aflatoxin, ochratoxin and patulin and would be useful as benchmark information for development future research.