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• Twenty-seven grain samples of Andean pseudocereals were profiled by LC-HRMS. • Untargeted metabolomics was used to differentiate varieties from the whole metabolome dataset. • Five mycotoxins were quantify using targeted metabolomics. • Sixteen samples from Peru and one sample from France were contaminated with Beauvericin. • An inventory of the fungal community infesting the Andean pseudocereal samples was documented. Pseudocereals are best known for three crops derived from the Andes: quinoa (Chenopodium quinoa), canihua (C. pallidicaule), and kiwicha (Amaranthus caudatus). Their grains are recognized for their nutritional benefits; however, there is a higher level of polyphenism. Meanwhile, the chemical food safety of pseudocereals remains poorly documented. Here, we applied untargeted and targeted metabolomics approaches by LC-MS to achieve both: i) a comprehensive chemical mapping of pseudocereal samples collected in the Andes; and ii) a quantification of their contents in emerging mycotoxins. An inventory of the fungal community was also realized to better know the fungi present in these grains. Metabotyping permitted to add new insights into the chemotaxonomy of pseudocereals, confirming the previously established phylotranscriptomic clades. Sixteen samples from Peru (out of 27) and one from France (out of one) were contaminated with Beauvericin, an emerging mycotoxin. Several mycotoxigenic fungi were detected, including A spe rgillus sp., Penicillium sp., and Alternaria sp. [ABSTRACT FROM AUTHOR]