Food safety may be compromised by the presence of chemical contaminants, such as mycotoxins and pesticide residues. Mycotoxins are natural contaminants produced by certain species of filamentous fungi and can cause toxic effects on human health. Pesticide residues are any specified substance in food resulting from the use of a pesticide with toxicological significance. To protect consumers from these toxic substances, different food regulatory agencies have set maximum levels permitted in different raw materials and processed foods. However, recent research has demonstrated a high incidence of both mycotoxins and pesticide residues (not simultaneously) in foods marketed all around the world, sometimes with levels above the regulated limits. One way to reduce such contaminants is to use ozone (O3) in food processing. Due to its high potential as an oxidant, O3 or the radicals generated in the ozonation process react with mycotoxins and pesticide residues that lose their toxicity due to molecular degradation. In this review paper the recent research into using O3 for gaseous ozonation and ozonized water to decontaminate food by eliminating and/or reducing mycotoxins and pesticide residues are discussed. Also the changes promoted in food quality attributes, the possible formation of degradation products of toxic relevance, as well as some perspectives for the future use of this technology in food processing are explored.