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Soil carbon (C) storage potential has received considerable attention for its role in climate change mitigation, and much research work has been devoted to studying the effect of land-use change, including land abandonment, on carbon dynamics. A comparative analysis of soil organic carbon (SOC), easily extractable Bradford-reactive soil protein (EE-BRSP) and Bradford-reactive soil protein (BRSP) was carried out at monthly intervals in a land-use sequence including cultivated soils, forest soils, shrubs and pasture in northeast Spain. In general, greater seasonal variations of both EE-BRSP and BRSP were found in soils with less carbon storage capacity. Turnover of glomalin into more stable C forms was associated with a small EE-BRSP:BRSP ratio in better structured soils and BRSP was related to organic carbon, suggesting positive contributions to both the recalcitrant carbon pool and soil structure. This effect seemed to be more pronounced in August when more BRSP was found, probably because of high temperature and dry soils in which glomalin may react to preserve residual adsorbed water and provide better protection in soil microsites. The role of glomalin was further enhanced by the structural stability of aggregates (WSA) investigated in two aggregate fractions (0.25–2.00 and 2.00–5.60 mm), indicating its beneficial effect in aggregation and carbon storage potential. BRSP, SOC and WSA increased significantly (P < 0.001) along the transect and abandonment sequence; the largest WSA values were generally greater in summer in both aggregate fractions. However, values in cultivated soils were always smaller than in soils under shrubs and pasture. Similarly, soils with a smaller carbon pool had the largest proportion of carbon loss as CO2-C when land use changes from vines to pasture. The role of aggregates in protecting organic carbon against mineralization was therefore postulated and highlighted the importance of soil monitoring after land abandonment.