Nowadays, pseudo-cereals’ consumption is increasing due to their health benefits as they possess an excellent nutrient profile. Whole pseudo-cereal grains are rich in a wide range of compounds, namely flavonoids, phenolic acids, fatty acids, and vitamins with known beneficial effects on human and animal health. Mycotoxins are common contaminants in cereals and by-products; however, the study of their natural occurrence in pseudo-cereals is currently scarce. Pseudo-cereals are similar to cereal grains; thus, mycotoxin contamination is expected to occur in pseudo-cereals. Indeed, mycotoxin-producing fungi have been reported in these matrices and, consequently, mycotoxin contents have been reported too, especially in buckwheat samples, where ochratoxin A and deoxynivalenol reached levels up to 1.79 μg/kg and 580 μg/kg, respectively. In comparison to cereal contamination, mycotoxin levels detected in pseudo-cereal samples are lower; however, more studies are necessary in order to describe the mycotoxin pattern in these samples and to establish maximum levels that ensure human and animal health protection. In this review, mycotoxin occurrence in pseudo-cereal samples as well as the main extraction methods and analytical techniques to determine them are described, showing that mycotoxins can be present in pseudo-cereal samples and that the most employed techniques for their determination are liquid and gas chromatography coupled to different detectors.