The production of leavened bread is an important aspect of culture and nutrition worldwide and has been produced since at least the second millennium BCE. Despite bread’s integral role in society, the evolutionary history of the organisms central to breadmaking remain largely unexplored. Saccharomyces cerevisiae is the most common yeast in sourdough starters and is used exclusively in commercial bread baking. Breadmaking presents a number of selection pressures for yeast, including osmotic stress, metabolism of complex sugars, selection for particular aromas and tastes, and competition with a mixed microbial community. To understand how S. cerevisiae has adapted to these conditions, we have isolated and sequenced 47 S. cerevisiae strains from sourdough starters collected as part of a citizen science project from home-bakers across North America. We combine our sourdough strain genome sequencing with sequences representing a wide variety of fermentation and natural isolation sources to understand how adaptation to human-associated environments has shaped the genomes of S. cerevisiae. We characterize the population structure of S. cerevisiae found in sourdough starters and identify genomic signatures indicative of domestication in breadmaking yeast. We pair these population genomic analyses with phenotypic data collected on our sourdough strains and a selection of commercial baking strains, beer, sake, wine, and natural isolates to quantify dough rise, growth in the complex sugar maltose (prevalent in dough), and other baking traits. This study elucidates genetic and phenotypic traits under selection in S. cerevisiae as it has adapted to the unique bread dough environment.