AbstractLocal environmental conditions influence the occurrence and abundance of populations, and therefore, the contribution of the same species to the ecological structure and processes of communities can vary in different environments. We investigated the influence of the substrate on the intraspecific population structure of four shrub‐tree species from the Brazilian savanna (Aspidosperma tomentosum, Byrsonima pachyphylla, Davilla elliptica, and Ouratea hexasperma) that occur in adjacent areas, but under different environmental conditions: in shallow soils with rocky outcrops and steep relief in Rupestrian Savanna, and in deep soils and flat relief in Typical savanna. We hypothesized that the relief and physical–chemical conditions of the soil in the Rupestrian Savanna limit the establishment and development of species regarding the abundance of individuals and the horizontal and vertical structure of populations. We found that in the Rupestrian Savanna, the soil has higher levels of total cation exchange capacity and phosphorus, while in Typical Savanna, it is associated with higher pH, base saturation, and clay levels. We show that intraspecific variations do not differ between the two environments in number of individuals, average values of trunk diameter, and total plant height. We observed that the same species contributes in different ways to the structuring of communities in both environments. Our hypothesis was rejected because the population structure was not molded by the substrate type. We conclude that the shrub‐tree species seem to find adaptive alternatives to colonize the different types of substrates, for example, establishing in less stressful microhabitats on the rocky environments.