Proactive silviculture treatments (e.g., thinning) may increase C sequestration contributing to climate change mitigation, although, there are still questions about this effect in Mediterranean pine forests. The aim of this research was to quantify the storage of biomass and soil organic carbon in Pinus forests along a climatic gradient from North to South of the Iberian Peninsula. Nine experimental Pinus spp trials were selected along a latitudinal gradient from the pre-Pyrenees to southern Spain. At each location, a homogeneous area was used as the operational scale, and three thinning intensity treatments: unthinned or control (C), intermediate thinning (LT, removal of 30–40% of the initial basal area) and heavy thinning (HT, removal of 50–60%) were conducted. Growth per unit area (e.g., expressed as basal area increment-BAI), biomass, and Soil Organic Carbon (SOC) were measured as well as three sets of environmental variables (climate, soil water availability and soil chemical and physical characteristics). One-way ANOVA and Structural Equation Modelling (SEM) were used to study the effect of thinning and environmental variables on C sequestration. Biomass and growth per unit area were higher in the control than in the thinning treatments, although differences were only significant for P. halepensis. Radial growth recovered after thinning in all species, but it was faster in the HT treatments. Soil organic carbon (SOC10, 0–10 cm depth) was higher in the HT treatments for P. halepensis and P. sylvestris, but not for P. nigra. SEM showed that Pinus stands of the studied species were beneficed by HT thinning, recovering their growth quickly. The resulting model explained 72% of the variation in SOC10 content, and 89% of the variation in silvicultural condition (basal area and density) after thinning. SOC10 was better related to climate than to silvicultural treatments. On the other hand, soil chemical and physical characteristics did not show significant influence over SOC10- Soil water availability was the latent variable with the highest influence over SOC10. This work is a new contribution that shows the need for forest managers to integrate silviculture and C sequestration in Mediterranean pine plantations.