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Mycotoxins are naturally occurring toxic secondary metabolites produced by filamentous fungi contaminating various food and feed crops. Exposure to mycotoxins has been associated with mycotoxicosis, which accounts for a high percentage of diseases in developing countries where methods of food handling and storage are inadequate. For the first time, this study determined the diversity, prevalence and co-occurrence of mycotoxins across the beans value chain in Eswatini. A total of 226 beans samples received between 2001 and 2021 by mycotoxin laboratory at Malkerns research were analysed and more than 59.3% of the samples were found contaminated with mycotoxins. Results confirmed that aflatoxins (AFs) and Zearalenone (ZEN) were the main contaminating mycotoxins in beans. These mycotoxins occurred singly and co-occurred as mixtures in the samples analysed. Considerable differences regarding the prevalence of these mycotoxins were observed between samples from different beans value chain actors and between sampling years. Implications of the results on the pre and postharvest handling of beans in Eswatini and the health hazard that mycotoxins pose to humans and animals were discussed. The importance of clear and enforceable regulations on levels of mycotoxin in beans and other dietary products is emphasised and the need for research on the deleterious effects of mycotoxins and their metabolites on animal and human health is underlined.