Unhygienic handlings of several African food products during storage have been reported to promote fungal biodeterioration and subsequent aflatoxin contamination. Therefore, this study was aimed to investigate the effect of storage time on nutrient, commonly associated bio-deteriorating fungi and aflatoxin contents of selected vegetables; Bitter leaf (Vernonia amygdalina) and Jute (Corchorus olitorius) in Nigeria. Fresh and stored vegetable samples (24) were collected from different markets in Ibadan, Nigeria, they were analyzed for proximate (% Moisture, Carbohydrate, Crude Protein, Fat and Fibre), nutrient (Potassium, Calcium, Phosphorus, Sodium Iron, Zinc and Magnesium), fungal and aflatoxin contents (AFB1, AFB2, AFG1 and AFG2). Most dominantly associated fungal strains were identified as Aspergillus niger, Aspergillus flavus, Aspergillus terreus, Aspergillus tamari, Aspergillus parasiticus, Aspergillus fumigatus, Penicillium chrysogenum and Rhizopus nigricans. The fungal incidence was more pronounced in the stored samples as compared to the fresh samples. The storage time also significantly affected the nutrient and aflatoxin contents of the vegetables; most nutrients decreased with increasing storage period while the aflatoxin contents increased. The study affirms that the storage time has effect on the nutrient, fungal contamination and consequently on the associated aflatoxin, although the detected aflatoxin levels were below the tolerance limit but these may increase with the storage time. It is therefore advisable to take hygienic measures during storage period and also, prolong storage should be discouraged.