The presence of mycotoxins in food products is a major worldwide problem. Nowadays, mycotoxins can only be detected by the use of sample-based chemical analyses. Therefore, we demonstrate the use of one- and two-photon-induced fluorescence spectroscopy for the non-destructive detection of mycotoxins in unprocessed food products. We first explain our optical set-up, which is able to measure the localized one- and two-photon-induced fluorescence spectra. Following, as a case study, the detection of aflatoxin in maize kernels is discussed. We present our research methodology, from the characterization of the fluorescence of pure aflatoxin, to the study of the one- and two- photon-induced fluorescence spectra of maize kernels and the development of an optical detection criterion. During both one- and two-photon-induced fluorescence processes, the fluorescence of the aflatoxin influences the intrinsic fluorescence of the maize. Based on the fluorescence spectrum between 400 and 550 nm, a detection criterion to sense the contaminated kernels is defined. Furthermore, we successfully monitored the localized contamination level on the kernel’s surface, showing both contaminated kernels with a high contamination in a limited surface area (a few square millimetres) and kernels with a low contamination spread over a large surface area (up to 20 mm2). Finally, the extensibility of our research methodology to other fluorescent mycotoxins is discussed.