The selection of species for restoration projects requires decision-making to be based on scientific evidence as well as input and approval from local communities. To better guide future restoration initiatives, this study assessed the socio-ecological effects of two Prosopis congeners including the native Prosopis cineraria and the non-native P. juliflora (mesquite) in two different sites in Southern Iran. Soil parameters including pH, electrical conductivity, organic carbon, and total nitrogen as well as vegetation indices including native vegetation cover, diversity, and density were measured under both of the congener tree species. Furthermore, pastoralists' perceptions toward the colonizing ability of both Prosopis congeners, their impacts on ecosystem services, and people's livelihoods and human well-being were assessed through interviews and semi-structured questionnaires. The ecological results showed that areas with native P. cineraria had higher native vegetation cover, density, and diversity as compared to sites with the non-native P. juliflora. Soils under P. cineraria and P. juliflora generally showed similar properties, with some small differences between sites (especially for pH and nitrogen). The social results showed that pastoralists in both study regions perceived P. cineraria to be better for local ecosystem services and livelihoods and viewed it to have lower colonizing or invasion potential. It can be concluded that native P. cineraria is a better candidate for restoration because it provides more ecological and social benefits and poses fewer long-term threats. Caution should be taken when promoting non-native species such as P. juliflora for restoration.