Soil aggregation and organic matter of soils from the pre-Pyrenean range in Catalonia (NE Spain) were studied, in order to assess their quality as carbon sinks and also to select the best soil management practices to preserve their quality. Aggregate stability, organic carbon and micromorphology were investigated. The highest amount of organic carbon was found in alluvial, deep soils (228 Mg C ha−1), and the lowest was in a shallow, stony soil with a low plant cover (78 Mg C ha−1). Subsurface horizons of degraded soils under pastures were the ones with smaller and less-stable aggregates. Fresh residues of organic matter (OM) were found mostly in interaggregate spaces. Within the aggregates there were some organic remains that were beginning to decompose, and also impregnative nodules of amorphous OM. Although OM was evenly distributed among the aggregate fractions, the larger blocky peds had more specific surface, contained less decomposed OM and had a lower organic/mineral interphase than smaller crumb aggregates, which were also more stable. Soil carbon storage was affected primarily by the OM inputs in the surface horizons. In order to store organic carbon over the mid- and long-term periods, the mechanisms favouring structuration through biological activity and creating small aggregates with intrapedal stable microporosities seemed to be the most effective.