In this study, melon (n = 60) and sesame (n = 60) seeds purchased from markets within Benue and Nasarawa states, respectively, in Nigeria, during two seasons (dry and wet), were analysed for fungal and mycotoxin contamination in order to determine the safety of these foods for human consumption. Molecular analysis revealed the following seven fungal taxonomic groups in the foods: Aspergillus section Candidi, Aspergillus section Flavi, Aspergillus section Nigri, Cladosporium, Fusarium fujikuroi species group, Penicillium, and Pleosporales/Didymellaceae. A total of 78 microbial metabolites, including several mycotoxins, occurred in the foods. The most frequent mycotoxins in melon and sesame were aflatoxin B1 (occurrence: 76%) and alternariol monomethyl ether (occurrence: 59%), respectively. However, higher mean total aflatoxin levels occurred in sesame (17 μg kg−1) than in melon (11 μg kg−1). About 28 and 5% of melon and sesame, respectively, exceeded the 4 μg kg−1 total aflatoxin limit for oilseeds intended for direct human consumption in the European Union. Additionally, fumonisin B1 and moniliformin occurred only in sesame, whilst ochratoxins A and B occurred only in melon; ochratoxin B being reported for the first time in this food. Our data indicated seasonal variations in the fungal and mycotoxin contamination levels in both foods.