The consumption of high-quality Andean grains (a.k.a. pseudocereals) is increasing worldwide, and yet very little is known about the susceptibility of these crops to mycotoxin contamination. In this survey study, a multi-analyte liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was utilised to determine mycotoxin and fungal metabolite levels in Andean grains (quinoa and kañiwa) in comparison to cereal grains (barley, oats and wheat), cultivated in both South American (Bolivia and Peru) and North European (Denmark, Finland and Latvia) countries. A total of 101 analytes were detected at varying levels, primarily produced by Penicillium spp., Fusarium spp. and Aspergillus spp., depending on the type of crop, geographical location and agricultural practices used. Generally, Andean grains from South America showed lower mycotoxin contamination (concentration and assortment) than those from North Europe, while the opposite occurred with cereal grains. Mycotoxin contamination profiles exhibited marked differences between Andean and cereal grains, even when harvested from the same regions, highlighting the need for crop-specific approaches for mycotoxin risk mitigation. Lastly, the efficacy of grain cleaning in respect to total mycotoxin content was assessed, which resulted in significantly lower levels (overall reduction approx. 50%) in cleaned samples for the majority of contaminants.