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Arid and semi-arid ecosystems dominate the R_S variability due to the multiple changing factors that control it. Consequently, any variation, in addition to climate change and land use change, impacts the concentration of CO₂ in the atmosphere. Here, the effect of the interannual variation and the controlling factors of R_S in native xeric shrublands and agricultural systems is investigated. This study was conducted in four sites per condition for two years (2019 to 2020), where R_S and the soil properties were measured. The R_S presented a higher variation in the xeric shrubland. The agricultural plots showed the highest R_S (0.33 g CO₂ m⁻² hr⁻¹) compared to the xeric shrubland (0.12 g CO₂ m⁻² hr⁻¹). The soil water content was the main controlling variable for R_S in both land uses. However, soil temperature affected R_S only in agricultural plots. The variation in the R_S under different land uses confirms that changes in the soil and environmental conditions (i.e., season) control the R_S. In addition, if current management practices are maintained in agricultural sites and under a temperature increase scenario, a significant increase in the R_S rate is expected.