Global climate change, as a consequence of the increasing levels of atmospheric CO2 concentration, may significantly affect both soil organic C storage and soil capacity for C sequestration. CarboSOIL is an empirical model based on regression techniques and developed as a geographical information system tool to predict soil organic carbon (SOC) contents at different depths. This model is a new component of the agro-ecological decision support system for land evaluation MicroLEIS, which assists decision-makers in facing specific agro-ecological problems, particularly in Mediterranean regions. In this study, the CarboSOIL model was used to study the effects of climate change on SOC dynamics in a Mediterranean region (Andalusia, S Spain). Different downscaled climate models were applied based on BCCR-BCM2, CNRMCM3, and ECHAM5 and driven by SRES scenarios (A1B, A2 and B2). Output data were linked to spatial data sets (soil and land use) to quantify SOC stocks. The CarboSOIL model has proved its ability to predict the short-, medium- and long-term trends (2040s, 2070s and 2100s) of SOC dynamics and sequestration under projected future scenarios of climate change. Results have shown an overall trend towards decreasing of SOC stocks in the upper soil sections (0-25 cm and 25-50 cm) for most soil types and land uses, but predicted SOC stocks tend to increase in the deeper soil section (0-75 cm). Soil types as Arenosols, Planosols and Solonchaks and land uses as "permanent crops" and "open spaces with little or no vegetation" would be severely affected by climate change with large decreases of SOC stocks, in particular under the medium-high emission scenario A2 by 2100. The information developed in this study might support decision-making in land management and climate adaptation strategies in Mediterranean regions, and the methodology could be applied to other Mediterranean areas with available soil, land use and climate data. © Author(s) 2013.