In semiarid agroecosystems of the Ebro valley (NE Spain) soils are characterized by low soil organic matter (SOM) and a weak structure. In this study we investigated the individual and combined effect of tillage system (no‐tillage, NT; reduced tillage, RT; conventional tillage, CT) and cropping system (barley–fallow rotation at the Peñaflor site, PN‐BF and continuous barley at the Peñaflor site, PN‐BB) on soil organic carbon (SOC) storage as well as the physical protection of SOM fractions by soil aggregates in three long‐term experimental sites. In both cropping systems, total SOC content was more than 30% higher in NT compared with CT in the 0‐ to 5‐cm depth. The suppression of fallowing in the PN‐BB cropping system led to a greater SOC stabilization only in NT. In all the three sites, greater proportion of water‐stable macroaggregates (>250 μm) was found under NT than under CT in the 0‐ to 5‐cm depth. Macroaggregate organic C concentration (250–2000 μm) was greater in NT compared with CT in the BB cropping system, but did not differ with tillage treatment in the PN‐BF rotation. Greater proportion of microaggregates within macroaggregates in NT compared with CT was only found in the Agramunt site (AG). However, greater C stabilized inside these microaggregates was observed in AG, Selvanera site (SV), and PN‐BB in the 0‐ to 5‐cm depth. The results of this study demonstrate that in the semiarid Mediterranean agroecosystems of the Ebro valley, the adoption of NT together with the suppression of long‐fallowing period can significantly increase the amount of SOC stabilized in the soil surface and improve soil structure and aggregation.