Cacti provide ecosystem services and mitigate climate change. Some cacti are endemic to Mexico. One example is Stenocereus queretaroensis (family Cactaceae), which also has commercial value for the local community in the Chapala subbasin. The objectives of this work were to determine the ecological niche and potential distribution of S. queretaroensis and to identify the ideal areas for its conservation and use in the Chapala subbasin. Four types of predictors were used: climate, soil properties, vegetation indices, and relief attributes. Presence and absence data were obtained during the field work. Comparison of means and principal component analysis were applied to the environmental predictors to determine the ecological niche of this species. The potential distribution of this species was predicted using an ensemble of six algorithms and five suitability classes. The results of both the mean comparison test and principal component analysis revealed that eight variables define the ecological niche of S. queretaroensis. The highly suitable and moderately suitable classes are concentrated in the central part of the studied subbasin, specifically around the periphery of Lake Chapala, as well as in the northeastern and southeastern regions of the basin. Areas with leptosols, which have shallow soils and good drainage, are the most suitable for S. queretaroensis conservation.