Carbon dynamics in deep layers have potential for soil C sequestration and contribute to the fight against global climate change, however, in Mediterranean regions, most studies focus on the top 20-30 cm soil layer. To advance this knowledge, this study proposes to investigate the behavior of different SOC compartments in the topsoil (0-15 cm) and subsoil (15-60 cm) in two rainfed almond orchards under conditions typical of Mediterranean regions. The treatments evaluated included seeded cover crops (SCC), and spontaneous cover crops (NCC) combined with reduced tillage and traditional tillage (TT). Moreover, an undisturbed natural reference area (forest) representing the pre-cultivated conditions was included. Samples from two experimental sites (Burete and Cagitan) were collected at intervals of 0-15, 15-30, 30-50 and 50-60 cm, and quantified bulk density, soil organic carbon (SOC), particulate organic carbon (POC) and Nitrogen (PON), hot water extractable carbon (HWOC) and short-term mineralizable carbon (SMC). The results showed that the use of cover crops and reduced tillage improve microbial activity, increase soil organic matter fractions, and improve carbon storage, both in the topsoil and subsoil, being an effective and useful strategy for the improvement of soil C sequestration under rainfed almond crop systems in semi-arid areas. In addition, the positive effect of cover crops on SOC storage would have been underestimated by about 35-40 % without accounting for the stock at the 30-60 cm layer. The use of different organic carbon and nitrogen fractions has furthered the understanding of soil carbon dynamics and proved effective in detecting differences among soil management strategies.