Aflatoxins are among the main carcinogens threatening food and feed safety while imposing major detection challenges to the agrifood industry. Today, aflatoxins are typically detected using destructive and sample-based chemical analysis that are not optimally suited to sense their local presence in the food chain. Therefore, we pursued the development of a non-destructive optical sensing technique based on fluorescence spectroscopy. We present a novel compact fluorescence sensing unit, comprising both ultraviolet excitation and fluorescence detection in a single handheld device. First, the sensing unit was benchmarked against a validated research-grade fluorescence setup and demonstrated high sensitivity by spectrally separating contaminated maize powder samples with aflatoxin concentrations of 6.6 µg/kg and 11.6 µg/kg. Next, we successfully classified a batch of naturally contaminated maize kernels within three subsamples showing a total aflatoxin concentration of 0 µg/kg, 0.6 µg/kg and 1647.8 µg/kg. Consequently, our novel sensing methodology presents good sensitivity and high potential for integration along the food chain, paving the way toward improved food safety.