A multiclass analytical method to determine pesticides and mycotoxins in beer-related matrices based on the dilute and shoot approach was optimized and validated according to the European guidelines SANTE/12682/2019 and EC/401/2006. Extraction used acidified acetonitrile at 1% (v/v) acetic acid, followed by horizontal shaking homogenization, centrifugation, freeze-out step for cleanup, another centrifugation, and injection into a high-performance liquid chromatography-tandem mass spectrometry system. Linearity, detection and quantification limits, accuracy, and measurement uncertainty were evaluated, and 201, 184, and 176 analytes were validated for malt, beer, and brewers' spent grain, respectively. The limits of quantification ranged between 1 and 200 μg kg and between 5 and 1000 μg kg for beer and malt, respectively, and expanded uncertainties ranged between 9.7 and 50%, meeting the legislation requirements. A total of 40 samples have been analyzed thus far, and 36 of them exhibited the presence of some of the analyzed substances. The validated method is reliable and easy to apply for mycotoxin and pesticide determination in complex matrices.