Soil organic matter (SOM) is a critical component of the soil system and a sensitive indicator of soil quality. We aimed to investigate the response of SOM pools to different land uses and management in irrigated croplands of the semi-arid region of northeast Brazil. Four sites irrigated under long-term (29 years) land uses were selected: banana (B1 and B2); elephant grass (EG) - perennial systems; maize and cowpea succession (MCP) - annual system; B1 was cropped for 17 years +2 years of maize and cowpea +17 years banana, while B2 was continuously cropped. A native forest (NF) site was selected as reference of steady state. Soil samples were collected at four depths in the rows and inter-rows of each management system. The higher decline in SOM fractions was perceived at 0–0.05 m depth and microbial indices (microbial biomass C and N, and basal respiration and metabolic quotient) were very sensitive indicators of soil quality. Perennial systems (B1 and EG) maintained the C and N stocks at higher levels equivalent to NF at the 0–0.40 m layer, while MCP and B2 had lower total organic carbon (TOC) (15 and 17%, respectively) and total nitrogen stocks (4.27 and 8.67%, respectively). Perennial cultivation with B1 and EG showed also the highest soil C and N microbial biomass and stratification ratio and, the lowest respiratory quotients, all indications of elevated soil C sequestration. In general, land use change from native forest to annual crops reduced plant residue input and increased soil disturbance, favoring higher SOM mineralization, while perennial crops and grasses were the most effective in increasing C and N stocks due to the maintenance of crop residues on the soil surface and the absence of soil tillage.