Mycotoxins and food allergens are growing health concerns in the area of food safety. Accidental exposure to mycotoxins and food allergens can arise in many ways including exposure to allergenic proteins due to cross-contamination, unspecified product labels and toxic residues through direct or indirect intake of contaminated food. In recent years, nanomaterials in various immunoassays have shown great potential to selectively detect mycotoxins and food allergens with lower detection limits and in a shorter time. This review compares the different immunoassay approaches, and discusses the recent applications of carbon and gold nanomaterials in developing immunoassays to detect mycotoxins and food allergens. Various types and shapes of carbon, spherical and non-spherical gold nanoparticles and their synthesis methods were elaborated. The different approaches on how these nanomaterials can be incorporated or used as a combination to improve the performance of immunoassays were addressed. Lastly, the challenges and prospects of detection of contaminants and allergens in food were discussed.