This study examines the prevalence of aflatoxin contamination in 160 nut samples, both shelled and unshelled (including pistachios, peanuts, and walnuts), from the Lebanese market, focusing on their fungal contamination and specific toxigenic strains. Aflatoxin B1 (AFB1), known for its potent carcinogenic and immunosuppressive properties, was detected in various samples. Moisture content analysis showed that unshelled nuts often exceeded maximum moisture limits more frequently than shelled nuts, with levels ranging from 1.9 to 9.5%. The predominant fungal genus identified through cultivation on potato dextrose agar (PDA) plates was Aspergillus. In total, 55% of samples were contaminated with A. flavus and 45% with A. niger. All toxigenic strains isolated were identified as Aspergillus flavus. The aflatoxins, particularly AFB1, were quantified using the enzyme-linked immunosorbent assay (ELISA) and reversed-phase high-performance liquid chromatography (HPLC), revealing contamination in 43.8% of the samples, with concentrations ranging from 0.4 to 25 µg/kg. Some samples notably exceeded the established maximum tolerable limits (MTLs) for AFB1, set between 2 and 8 µg/kg. Shelled pistachios showed the highest contamination rate at 52% and were the most frequent to surpass the MTL of 8 µg/kg for pistachios, whereas walnuts displayed the lowest contamination levels, with only 15.4% exceeding the MTL for aflatoxins.