Aqueous extract of ajowan seeds was found to contain an aflatoxin inactivation factor (IF). Thin layer chromatography analysis of the toxins after treatment with IF showed relative reduction of aflatoxin G1 > G2 > B1 > B2. Quantification of toxin using a fluorotoxin meter as well as the Enzyme Linked Immunosorbent Assay (ELISA) confirmed these findings. An approximate 80% reduction in total aflatoxin content over the controls was observed. This observed phenomenon of reduction in total toxin was referred to as toxin inactivation. Temperature was found to influence the rate of toxin inactivation. At 45 °C, it was found to be rapid during the initial 5 h and slowed later. The IF was found to retain considerable activity even after boiling and autoclaving, indicating partial heat stability. The activity was lost below pH 4.0. Above pH 4.0, it increased gradually, reaching the maximum at pH 10.0. IF was found to be stable to gamma irradiation. Toxin decontamination in spiked corn samples could be achieved using IF. This study emphasizes the potential of ajowan IF in aflatoxin removal from contaminated food commodities. However, the biological toxicity, if any, of the IF inactivated aflatoxins needs to be confirmed, and the work in this direction is in progress.