The purpose of this study is to investigate mitigation potential of tree-crop cultivations in the Mediterranean region and particularly in Spain, Italy and Greece. In that respect, a methodology is developed, built on top of different parameters affecting the sequestration in tree-crops and providing us with the vital compatibility to apply it in the Mediterranean region and set the framework up to generalize it for other regions in the future. The key parameters that were considered, are the tree-crop type, environmental conditions, the climatological conditions and the socioeconomic dimension of the cultivation. In that direction, field measurements for five representative tree-crops were made, and the relative management practices applied by the farmers were gathered with questionnaires. The current climatic conditions were collected as well as the future conditions were evaluated by projecting for the next 50 years with the use of a Global Climate Model. Based on these, an estimation algorithm was developed (CO2 Removal Capacity Algorithm) that captures the yearly CO2 balance in Biomass, Soil and the enclosed management practices and can be applied specifically at different regions of the study area. As a result, different cultivation practices are evaluated, and their mitigation potentials accordingly ranked. Our study identifies certain mitigation potentials of the agricultural sector and hence contributes to the development of climatic policies coupling agricultural, economic and climatic objectives.