Beer is one of the most popular beverages worldwide. As a product of variable agricultural ingredients and processes, beer has high molecular complexity. We have used integrated proteomics, metabolomics, and genomics to investigate the molecular complexity and diversity throughout the beer making process. We uncovered substantial variability in barley based on variety and growth environment, and found that proteolysis during the mashing stage of beer production controls protein thermal stability and abundance in the final beer. Profiling 23 commercial Australian beers identified a very high diversity of post-translational modifications (PTMs), especially proteolysis, glycation of barley proteins, and glycosylation of yeast proteins. The key differentiator of the beer glyco/proteome was the brewery, with beer from independent breweries having a distinct profile to beer from multinational breweries. Within a given brewery, beer styles had distinct glyco/proteomes, with proteins in darker beers having low glycation and high proteolysis. Quantitative quality metrics of foam formation and stability correlated with the concentration of abundant surface-active proteins from barley and yeast. Finally, to expand the flavour and sensory profiles after fermentation we have used proteomics, genomics, and metabolomics to investigate wild yeast ferments for controlled production of diverse beer styles.