Peanuts are likely to be infested by fungi with consequent contamination by aflatoxin in post-harvest industries. A hazard analysis critical control point (HACCP) plan is proposed for a typical Brazilian post-harvest industry from raw in-shell reception to the unpeeled peanuts transportation. Codex Alimentarius Commission guidelines were followed, with four critical control points (CCP) for aflatoxin being identified. The process steps with highest probability of aflatoxin occurrence (risk) are the in-shell reception, the dried in-shell storage, and the unpeeled kernel storage. During the storage steps there is a lack of control of air moisture and temperature. Therefore, there is no option but to keep rigid monitoring and control over each CCP, and detour lots with high aflatoxin levels to either oil or seed production. Attempts to correlate the aflatoxin levels with the rainfall showed an irregular trend of the toxin level.