In croplands, the adoption of certain management practices may increase soil organic carbon (SOC) levels. In this study, we evaluated the short-term impact of crop stover management and the interaction between crop stover and irrigation method on SOC change in a continuous maize (Zea mays L.) system in Spain. Four years after the beginning of the experiment, total SOC and C fractions (particulate organic matter carbon, POM-C; and mineral-associated organic matter carbon, Min-C) contents, SOC stocks and SOC stock changes were measured in four different soil layers (0−5, 5−10, 10−25 and 25−50 cm) in an experiment with two irrigation methods (sprinkler and flood) and three stover management systems (conventional tillage with all the stover incorporated, CT; no-tillage maintaining the stover, NTr; and no-tillage removing the stover, NT). Stover management resulted in significant differences in SOC and POM-C but not in Min-C. In particular, NT reduced SOC and POM-C contents compared with CT and NTr (about 10 and 60 %, respectively). After 4 years, SOC change was not affected by the interaction between stover management and irrigation. Concurrently, both CT and NT showed SOC losses, reaching 0.11 and 1.22 Mg ha−1 yr−1 in CT and NT, respectively. However, NTr showed SOC gains at a rate of 0.09 Mg ha−1 yr−1. Consequently, the removal of crop stover has been demonstrated as a detrimental strategy to store SOC in the short-term in irrigated continuous maize systems.