Molds of the genus Fusarium infect nearly all types of grain, causing significant yield and quality losses. Many species of this genus produce mycotoxins, which pose significant risks to human and animal health. In beer production, the complex interaction between primary fungal metabolites and secondarily modified mycotoxins in barley, malt, and beer complicates the situation, highlighting the need for effective analytical methods to quickly and accurately monitor these toxins. We developed and validated a liquid chromatography-tandem mass spectrometry (LC–MS/MS) method to simultaneously analyze 14 Fusarium toxins, including modified forms (deoxynivalenol (DON), DON-3-glucoside, 3-acetyl-DON, 15-acetyl-DON, nivalenol, fusarenone X, HT-2 toxin, T-2 toxin, the enniatins A, A1, B, B1, beauvericin, and zearalenone) in barley and throughout the malting process. Stable isotope dilution assays (SIDAs) and matrix-matched calibration were used for quantification. A micro-malting setup was established to produce Fusarium-contaminated barley malt under reproducible conditions using targeted inoculation with F. culmorum. Mycotoxins were quantified throughout the malting process and compared to the content of fungal DNA. Further, the impact of various malting parameters was investigated, thus revealing that different malting scenarios exhibited different toxin enrichment patterns. We demonstrated that mycotoxin concentration and the ratio of DON to DON-3-glucoside changed throughout the malting processes, depending on fungal spore concentrations, germination temperature, and malting temperature. The study highlights the complexity of mycotoxin dynamics in malt production and the importance of optimized processing conditions to minimize toxin levels in final malt products.