Fungal infections and mycotoxin contamination in food products pose a major threat to the world population. Mycotoxins contaminate approximately 25% of the world’s food products and cause severe health problems through the utilization of affected food products. The major mycotoxins in different foods are aflatoxins, ochratoxins, fumonisins, zearalenone, trichothecenes, and deoxynivalenol. Today, various conventional and nondestructive techniques are available for the detection of mycotoxins across multiple food products. Conventional methods are time-consuming, require chemical reagents, and include many laborious steps. Therefore, nondestructive techniques like near-infrared (NIR) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, hyperspectral imaging, and the electronic nose are a priority for online detection of fungal and mycotoxin problems in different food products. In this article, we discuss recent improvements and utilization of different nondestructive techniques for the early detection of fungal and mycotoxin infections in various food products.