Because of its profound importance in the fermentation of foods and beverages, the link between humans and the yeast Saccharomyces cerevisiae is tight and ancient. Yeast strains associated with modern winemaking reflect a history of dispersal by human activity, which has produced a population of limited genetic diversity that resides in vineyards around the globe. Here, we examine whether the same might be true of the microorganisms associated with other crops that have been transported by humans and whose products rely on fermentation, specifically coffee and cacao. We focus on one of these microbes and show that live strains of S. cerevisiae can be isolated from unroasted coffee and cacao beans long after they have been processed by fermentation in their countries of origin. Unlike the wine strains, coffee and cacao yeasts are genetically diverse and form discrete populations, demonstrating independent origins of distinct populations of yeast from the same human-associated activity. These populations show evidence of admixture events between three previously characterized populations, one of which is the wine population itself. Thus, our study suggests that human-associated fermentations and migration have affected the distribution and abundance of yeast used for the production of coffee and chocolate. While human transport of cultivated plants is well documented, our impact on associated microbes is only now becoming apparent.