Oats are of special interest due to their physiological properties and the fact that they can be consumed by most celiac patients. Oat beer could be a gluten-free alternative to traditional barley malt beer. Knowledge of protein changes during brewing is technologically relevant because they influence foam and haze formation. The aim of this study was to follow protein changes during brewing of common barley malt beer compared with an alternative made from oat malt. Two-dimensional gel electrophoresis and lab-on-a-chip analysis were used to obtain protein profiles of malts, worts, hot trubs, and beers. In barley beer, the most abundant proteins were detected, including protein Z, lipid transfer protein 1, and other low molecular weight proteins. In oat beer, protein profiles similar to those of barley beer were detected. Despite the different protein distribution in barley and oats (i.e., mainly prolamins and glutelins in barley and mainly globulins in oats), the resulting beers had similar protein profiles.