We investigated 16 fonio millet and 17 sesame samples by LC/ESI-MS/MS for the spectrum of microbial metabolites contaminating these seeds. Forty-eight fungal and four bacterial metabolites were detected in fonio, while 28 fungal and two bacterial metabolites were found in sesame. Altogether, 55 metabolites were identified in both grains, 18 of which are reported for the first time to naturally occur in cereals and oil seeds. The metabolite concentrations reached 7,280 lg/kg in fonio for aurofusarin and 64,600 lg/kg in sesame for kojic acid. Aflatoxin contaminated 81 % of fonio samples at concentrations less than the 4 lg/kg maximum allowable limit (MAL) set by European Union (EU). In contrast, aflatoxin was not detected in sesame. Zearalenone levels exceeded the EU MAL (75 lg/kg) in one sample of fonio (987 lg/kg). About 62.5 % (30 out of 48) of the metabolites without regulations occurred in more than 50 % of samples of one or both seeds, while 3-nitropropionic acid, beauvericin, brevianamid F, curvularin, emodin, equisetin, macrosporin A, monocerin and tenuazonic acid were the most prevalent, occurring in all samples of either fonio, sesame or both. This is the first study reporting mycotoxin contamination in sesame in Nigeria and the broad range of microbial metabolites in millet and sesame.