Filamentous fungi are recognized for their significance in food processing and antibiotic production, as well as their capacity to produce mycotoxins. Numerous secondary metabolites have been investigated, and their occurrence in foodstuffs, both in the field and during the storage of agricultural products, poses a substantial health risk to consumers. Several fungal species capable of producing mycotoxins have been documented. However, their presence suggests the potential occurrence of mycotoxins, of which only the most well-known are considered in health risk assessment, thus potentially underestimating the complex mixture to which consumers may be exposed. This review examines the range of secondary metabolites produced by Aspergillus species of the Flavi section found in agricultural products and foodstuffs. Known for their ability to produce aflatoxins, the presence of these fungi typically leads to the investigation of only aflatoxins, and possibly cyclopiazonic acid, in contaminated foods. This review elucidates the secondary metabolites produced by the Flavi section of Aspergillus and examines the associated hazards, to contribute to the assessment of the potential risk that the presence of these fungi in food products may represent.