Sorghum malts, which are important ingredients in traditional fermented beverages, are commonly infected by mycotoxigenic fungi and mycotoxins may transfer into the beverages, risking consumers’ health. Liquid chromatography–tandem mass spectrometry was used to determine variation of fungal metabolites in 81 sorghum malts processed for brewing of Namibian beverages, otombo (n = 45) and omalodu (n = 36). Co-occurrence of European Union (EU)-regulated mycotoxins, such as patulin, aflatoxins (B1, B2, and G2), and fumonisins (B1, B2, and B3) was detected in both malts with a prevalence range of 2–84%. Aflatoxin B1 was quantified in omalodu (44%) and otombo malts (14%), with 20% of omalodu malts and 40% of otombo malts having levels above the EU allowable limit. Fumonisin B1 was quantified in both omalodu (84%) and otombo (42%) malts. Emerging mycotoxins, aflatoxin precursors, and ergot alkaloids were quantified in both malts. Notably, 102 metabolites were quantified in both malts, with 96% in omalodu malts and 93% in otombo malts. An average of 48 metabolites were quantified in otombo malts while an average of 67 metabolites were quantified in omalodu malts. The study accentuates the need to monitor mycotoxins in sorghum malts intended for brewing and to determine their fate in the beverages.