Summary 1. Biological nitrogen (N) fixation by symbiotic and free‐living organisms is considered the main pathway for N soil enrichment in desert and semi‐desert ecosystems. This fact is more noticeable in tropical ecosystems where legume species have a high relative abundance. However, this biological fixation pathway does not guarantee the maintenance of soil N pools, and N conservation pathways are important in understanding controls over soil N cycling. 2. In dryland ecosystems, desert plants can form a ‘fertility island’ (FI) as soils beneath plants show higher concentrations of N and organic matter. 3. Here we assess how carbon (C) and N may interact to conserve soil N within the FI soil of two legume species (Prosopis laevigata and Parkinsonia praecox), one a known N‐fixer and the other believed not to fix N, as well as within adjacent bare ground soil. In a semi‐arid tropical ecosystem in central Mexico, we examined spatial patterns in C and N pools and transformation rates, and we investigated seasonal variations in these relationships. 4. Results show that FI soil C and N could be linked to total N storage through net C and N immobilization in microbial biomass and heterotrophic microbial activity. Soil under P. laevigata canopy had greater total N as well as N accumulated in microbial biomass than soil under P. praecox and bare ground soil. Nevertheless, inorganic N and potential net N mineralization rates were similar under soils of both species, although we expected higher inorganic N and N‐mineralization values in N‐fixer species to explain the greater total N. Higher total N concentrations under P. laevigata probably result from greater inputs of organic C and a higher potential net C mineralization rate in comparison to P. praecox and bare ground soil. 5. Even though N input and output values were not measured, the results highlight the importance of assessing the role of organic C, heterotrophic microbial activity, and N storage in microbial biomass in order to understand controls over N retention in soil N cycling. Thus, soil C‐N interactions could be a control factor of N soil conservation in this tropical semi‐arid ecosystem.