Recently, demand for fermented foods has increased due to their improved nutritional value, taste, and health-promoting properties. Worldwide consumption of these products is increasing. Fermented foods are generally safe for human consumption. However, some toxins, primarily biogenic amines (putrescine, phenylethylamine, histamine, tyramine, and cadaverine), mycotoxins (fumonisins, aflatoxins, ochratoxin A, zearalenone, and trichothecenes), and bacterial toxins (endotoxins, enterotoxins, and emetic toxins) can be produced as a result of using an inappropriate starter culture, processing conditions, and improper storage. These toxins can cause a multitude of foodborne illnesses and can lead to cardiovascular aberration and adverse gastrointestinal symptoms. Analytical techniques are in use for the detection of toxins in fermented foods for monitoring and control purposes. These include culture, chromatographic, immunoassays, and nano sensor-based techniques. These detection techniques can be used during the production process and along the food chain. On an industrial scale, HPLC is widely used for sensitive quantification of toxins in fermented foods. Recently, biosensor and nano sensor-based techniques have gained popularity due to accuracy, time efficiency, and simultaneous detection of multiple toxins. Other strategic methods being investigated for the removal of toxins from fermented foods include the use of specific starter cultures for bio-preservation, aflatoxin-binding, and biogenic amine-degradation agents that may help to appropriately manage the food safety concerns associated with fermented foods.