Organic agriculture can be a feasible alternative to improve soil organic carbon contents, but its effects on different carbon pools and the benefits for soil quality in sandy soils of warm climates are still poorly understood. This study aimed to assess the influence of organic and conventional farming systems on carbon pools, and its effects on soil chemical, physical, and biological quality in sandy soils of a semi‐arid region in northeastern Brazil. The experiment was conducted at three sites with different soil managements and adjacent natural vegetations in the municipality of Guaraciaba do Norte, Ceará, Brazil. Four soil profiles were opened, and soil samples were collected from 0 to 1 m depth for soil chemical analysis, and undisturbed soil samples from 0 to 40 cm depth for soil physical and micromorphological analysis. Organic management led to an increase in total organic carbon (from 7.34 to 20.47 g kg−1) at the 0–0.10 m depth, especially in the labile fraction. There was also a threefold increase in cation exchange capacity and up to a fourfold increase in P content in the soil surface layers. Additionally, organic systems led to better soil structure, porosity, and stability, as evidenced by an increase in the average diameter of soil aggregates. Within the aggregates, we found 240% more total organic carbon and 170% more total nitrogen in organic compared to conventional soil management. Micromorphological analysis allowed us to observe that soils under forestry and organic management have coarse quartz grains either totally or partially coated with clay by organic assemblage, while under conventional cultivation, there were reduced amounts of organic assemblages in the spaces between sand grains. Thus, organic farming is seen as a suitable practice for soil organic carbon formation in a short space of time (6 years), contributing to improving soil chemical quality and aggregation in sandy soils in semi‐arid northeastern Brazil.