Irrigation water restrictions in the Mediterranean area have created a growing interest in water conservation. Apart from environmental and economic benefits by water savings, regulated deficit irrigation (RDI) may contribute to reduce soil CO2 emissions and enhance C sequestration in soils, by decreasing microbial activity in response to decreased soil moisture levels. An experiment was established in an orchard for one year to investigate the effects of three irrigation strategies on soil CO2 emissions, soil C pool dynamics and aggregate content and stability. Three irrigation treatments were assayed: full irrigation (FI), RDI1, irrigated as FI except for the postharvest period where 50% of FI was applied; and severe RDI (RDI2), irrigated as RDI1, except for two periods in which irrigation was suppressed. Soil CO2 emissions were monitored every 15 d. Soil sampling was carried out every three months. Soil fractionation was also carried out (b50, 50–250, 250–850, 850–2000) to assess the weight, C content and aggregate stability of each fraction. The application of deficit caused a significant decrease in CO2 emission rates, mainly in RDI2, with rates of, in average, 35 mg CO2-C m−2 h−1 lower than that of FI during the period when deficit was applied. Cumulative CO2-C released for one year showed a total release of 410 g CO2-C m−2 in FI, 355 g CO2-C m−2 in RDI1, and 251 g CO2-C m−2 in RDI2. Soil organic C, recalcitrant C and organic functional groups showed no significant differences among treatments. The labile organic fractions increased under FI in summer, likely due to increments in microbial biomass C and enzyme activities. Irrigation treatments did not have a strong effect on the amount and stability of aggregates, but increased SOC content in the coarse fraction under RDI2. No effect of irrigation was observed in inorganic C content