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Craft breweries are continuously searching for beers made with locally produced raw materials and unique flavor profiles to respond to consumer requests. We explored the behavior of three commercial strains of <i>Saccharomyces cerevisiae</i> in the fermentation of ale beer with a high prevalence of rye malt in comparison to pure barley malt. In total, 34 volatile organic compounds were identified, with esters and alcohols being the quantitatively most abundant classes. The yeast strain appeared to impart more differences in the beer’s volatile profile compared to malt. In particular, <i>S. cerevisiae</i> var. <i>diastaticus</i> Y2 strain was associated with a higher production of esters, while strain <i>S. cerevisiae</i> Y3 was correlated to the higher amounts of terpenes together with the lowest relative abundance of volatile acids. Our findings encourage further investigation of the fermentation performance of several yeast strains to produce beers with unique flavors.