In mountain areas, water erosion plays an important role on soil structure and can strongly affect its functions. Suitable management practices, namely choice of crops, may be able to improve aggregate stability and reduce soil loss by surface runoff. To study the effects of cover crops on aggregation in mountain soils, we investigated a soil planted with wheat (site C) compared with two soils under alfalfa (sites A and B). All investigated soils were Typic Ustorthents. The soil aggregates were isolated by a physical-functional procedure defined on the basis of aggregate resistance against specific breakdown mechanisms such as slaking and water abrasion. One year after alfalfa plantation, its effect on wet aggregate stability and the amount of organic carbon (OC) and nutrients retained by the isolated aggregates were measured. In the less degraded soils (site B), organic matter decomposition was stimulated, and after 1 year, the total OC (TOC) and TOC/N declined. Consequently, a reduction in aggregate stability and ability to preserve elements occurred, as shown by the decrease of wet aggregate stability indexes and total nutrients (e.g. N, P and K) retained by stable aggregates. In more degraded soil (site A), alfalfa generally positively affected the investigated properties. The effect of alfalfa in the studied crop rotation depends on the degree of land degradation due to water erosion. As regards the investigated breakdown mechanisms, our data showed that the aggregate resistance to water abrasion was related to TOC, while the resistance against fast wetting breakdown is correlated to the microbial biomass.