The increasing consumption of plant-based products for health promotion or for disease treatment has generated public health concerns, since herbs or plants are in direct contact with soils and may easily be colonized by fungi. Many studies have shown the contamination of plant-based supplements and drugs with mycotoxigenic fungal species. Aspergillus and Penicillium species have been reported as the most frequent and dominant ones, with records of the occurrence of many mycotoxigenic species. The presence of different species raises the concern of multimycotoxin occurrence, while the increased consumption of these products increases exposure. This review aims to present updated data on the natural occurrence of mycotoxigenic fungi and their mycotoxins in plant-based supplements and medicines.