Sixty traditional leafy vegetables, comprising of mutete (Hibiscus sabdariffa) (n = 20) and omboga (Cleome gynandra) (n = 40) were analysed for fungal, plant and bacterial metabolites using liquid-chromatography-tandem mass spectrometry. No European Union legislated mycotoxins were quantified and no vegetables contained levels above the FAO/WHO limit of 10 mg/kg for cyanogenic potential, suggesting comparative safety regarding regulated mycotoxins and cyanogenic glycosides. Quantified fungal metabolites included averufin and 3-Nitropropionic acid from Aspergillus flavus, beauvericin and equisetin from Fusarium, citrinin and curvularin from Penicillium and altertoxin -1 and tentoxin from Alternaria. Of the plant cyanogenic glycosides, linamarin was quantifiable in 65% of mutete at a maximum of 398 µg/kg but not in omboga, while lotaustralin was quantifiable in both omboga and mutete. The bacterial metabolite nonactin was detected in 27.5% of omboga samples (range: 0.2-7.3 μg/kg). Minimal variation in metabolite patterns was recorded for omboga samples from Oshana and Oshikoto regions.