During the Quaternary, Chaco Phytogeographic Domain (Chaco) flora in subtropical South America experienced temperature and humidity fluctuations, primarily driven by wind dynamics, leading to significant shifts in species distribution. The palm Butia yatay is endemic to the Chaco and thrives in areas characterized by a warm–rainy climate and mostly restricted to sandy soils. To investigate the current geographic distribution of suitable habitat for B. yatay while assessing the significance of soil variables, we employed two distinct algorithms in species distribution modeling (SDM). We also determined whether the distribution of B. yatay has changed since the Pleistocene and whether these changes align with previously proposed Pleistocene refugia. In the present SDMs, we considered two separate sets of predictors, one set with bioclimatic variables only and the other set with bioclimatic topographic and soil variables. Additionally, we reconstructed the historical geographic distribution of suitable habitats using bioclimatic data. Our results suggested that the primary determinants of B. yatay's current distribution include precipitation and temperature of the driest month and soil cation exchange capacity. Incorporating soil variables affected the estimated size and range of suitable areas. Projections into the past indicated similar suitable habitat distributions during interglacial periods compared with the present. During the Last Glacial Maximum, climatically suitable habitat may have shifted northward, partially overlapping with previously suggested Pleistocene refugia located between the Paraná and Uruguay Rivers. These findings indicate the main factors driving the distribution and ecology of B. yatay and enhance understanding of subtropical flora shifts during the Quaternary. The approach also may prove valuable for other studies within the Chaco.