To assess the impact of black-colored grain on Alternaria mycotoxin concentrations in different stages of the brewing process, brewing experiments were conducted in a microscale brewhouse. Different mixtures of visually unaffected and black-colored batches of two malt samples were used, which were obtained by an optical sorting device. The 13 Alternaria mycotoxins alternariol (AOH), alternariol monomethyl ether (AME), tenuazonic acid (TeA), tentoxin (TEN), alterperylenol (ALTP), altertoxins I and II (ATX I and II), altenuene (ALT) as well as the modified forms AOH-3-glucoside (AOH-3-G), AOH-9-glucoside (AOH-9-G), AME-3-gluoside (AME-3-G), AOH-3-sulfate (AOH-3-S) and AME-3-sulfate (AME-3-S) were analyzed in each processing step by liquid chromatography–tandem mass spectrometry (LC–MS/MS), and the toxin concentrations were balanced over the whole brewing process. Fungal DNA content in the starting material (mixtures) was determined by quantitative real-time polymerase chain reaction (qPCR). In this study, TeA was the only toxin to migrate into the final beer, while the AOH, AME, TEN, ALTP and ATX I toxins were mainly found in the spent grains. The observance of AOH-3-S and AME-3-S in some processing steps also showed the possibility of modification reactions during brewing. Furthermore, no distinct correlations between the fungal DNA and the analyzed mycotoxins could be observed in the starting material, while the amount of black colored grains only impacted toxin concentrations in one of the two used malt samples. Nevertheless, it was shown that optical sorting of malt batches might be a useful tool for the malting and brewing industry to prevent elevated mycotoxin concentrations.