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The productivity of agricultural areas in semi-arid regions can be improved through the use of irrigation. However, the intensive cropping of such soils can have detrimental effects, especially with regard to soil organic matter (SOM) pools. The goal of this work was to evaluate soil organic carbon and nitrogen stocks of different irrigated agricultural systems and compare these to preserved natural ecosystems adjacent to each of the cropping systems. We selected four cropping systems: banana, a maize/bean succession (MB), pasture (P) and guava (G), as well as areas covered by native vegetation. Stocks of total soil organic carbon (TOC), amounts of unprotected and protected soil organic carbon, carbon and nitrogen in microbial biomass and microbial respiration were quantified. Surface soil TOC stocks under banana, G and P grass were significantly greater than under native vegetation and MB system. The most intensive management system was the MB, and the least intensive systems were P and G. The least intensive cropping systems were grouped on the basis of similarities in TOC, POC, total soil nitrogen and N in microbial biomass stocks. These results show that the degree of soil degradation resulting from changes in land use systems increases with the intensity of the land use systems themselves. This confirms the established hypothesis that the extent of degradation of soil properties and changes in some SOM fractions depend on the intensity of soil use. Furthermore, the adoption of conservation practices may remediate soil degradation and increase SOM stocks, mainly at the soil’s surface. Copyright (c) 2013 John Wiley & Sons, Ltd.