Plants are an important component in many natural ecosystems. They influence soil properties, especially in arid ecosystems. The selection of plant species based on their adaptations to site conditions is essential for rehabilitation of degraded sites and other construction sites such as check-dams. Other factors to be considered in species selection include their effects on soil properties and their abilities to meet other management objectives. The purpose of this study was to assess the effects of native (Populus euphratica Oliv. and Tamarix ramosissima Ledeb.) and introduced (Eucalyptus camaldulensis Dehnh. and Prosopis juliflora (Swartz) DC.) woody species on soil properties and carbon sequestration (CS) in an arid region of Iran. Soil sampling was collected at three soil depths (0–10, 10–20 and 20–30 cm) at the sites located under each woody species canopy and in an open area in 2017. Soil physical-chemical property was analyzed in the laboratory. The presence of a woody species changed soil characteristics and soil CS, compared with the open area. For example, the presence of a woody species caused a decrease in soil bulk density, of which the lowest value was observed under E. camaldulensis (1.38 g/cm3) compared with the open area (1.59 g/cm3). Also, all woody species significantly increased the contents of soil organic matter and total nitrogen, and introduced species had more significant effect than native species. The results showed that CS significantly increased under the canopy of all woody species in a decreasing order of P. euphratica (9.08 t/hm2)>E. camaldulensis (8.37 t/hm2)>P. juliflora (5.20 t/hm2)>T. ramosissima (2.93 t/hm2)>open area (1.33 t/hm2), thus demonstrating the positive effect of a woody species on CS. Although the plantation of non-native species had some positive effects on soil properties, we recommend increasing species diversity in plantations of native and introduced woody species to provide more diversity for the increased ecosystem services, resilience, health and long-term productivity.