A total of 779 samples of edible nuts (melon seeds, watermelon seeds, pumpkin seeds, and cantaloupe seeds) from southern cities of Punjab, Pakistan were collected from the summer and the winter seasons. The natural occurrence of aflatoxins (AFs) and vitamin E (tocopherols) levels were investigated using HPLC. The results have shown that 180 (43.4%) samples from the winter season and 122 (33.4%) samples from the summer season were found positive with AFs. The elevated average levels of total AFs (20.9±3.10 µg/kg) were observed in watermelon seeds without shell and the lowest average amount (15.9±3.60 µg/kg) were documented in melon seeds without shell samples from the winter season. The elevated average amount of total AFs 17.3±1.50 µg/kg were found in pumpkin seeds available as without shell. The results have documented a significant difference in total AFs levels in edible seeds available as shells versus without shells (α = 0.05 & 0.01). The highest dietary intake of 6.30 µg/kg/day was found in female individuals from pumpkin seeds (without shell) in the winter season and the value of 3.00 µg/kg/day were found in pumpkin seed without shell in summer season in female individuals. The highest amount of total tocopherol levels of 22.2 ± 7.70 ng/100g in pumpkin seeds samples from winter season and 14.5 ± 5.50 mg/100g were found in melon seeds samples from summer season. The variation of total tocopherol levels in edible seeds among the winter and summer seasons showed significant difference (p ≤ 0.0054), except watermelon seeds samples which shown non-significant difference (p ≥ 0.183).