Trace metals, particularly zinc, influence the growth and metabolism of yeast. In the literature the recommended concentration of zinc in pitching wort is > 0.15 mg/L; lower concentrations cause fermentation problems and reduce in consequence final beer quality. The aim of this study was the exploration of changes in bioavailability (available zinc), which was never considered before, and in the mass balance of total zinc during malting process and wort production. Therefore, the work comprised two parts: (1) investigating the effect of malt modification on zinc content and bioavailability of, respectively, produced malt depending on malt modification by varying the steeping degree (38–48%) in the malting process and (2) examining the effect of zinc losses and changes in bioavailability in the by-products (spent grain and hot break) by performing brewing trials up to pitching wort. Zinc was measured by atomic absorption spectroscopy. We applied a specific extraction scheme to evaluate first the bioavailability of zinc in brewing-related samples. In the malting process, total zinc losses increased with greater modification level of the malt samples, although bioavailability increased simultaneously. Spent grain was the primary zinc loss by-product (98%) in the brewing process. The distribution of the binding forms of zinc in hot break and spent grain was significantly altered with an increase in the less water-soluble binding forms of zinc.