Postharvest fungal diseases occurring during transportation and storage of fruits, vegetables, nuts and grains can lead to rotting and molding of different agricultural products and their associated products. Mycotoxins are hazardous secondary metabolites produced by fungi. Aflatoxins, Alternaria mycotoxins, Fumonisins, Ochratoxins, and Zearalenone are the major mycotoxins that pose a serious threat to human health. In order to remove the contamination of these potential hazardous substances and ensure food safety, detoxification methods including physical, chemical, and biological methods of mycotoxins are summarized in this work. Specially, biological strategies become a hot spot with safety and high efficiency characteristics. In addition, technologies for adsorbing and decomposing fungal toxins through yeast, enzymes, fungi, and bacteria are proved effective to eliminate fungal toxins. This work will contribute for better understanding of recent progress and future challenges for detoxification strategies for mycotoxins in foods.