<p>Mediterranean tree crops provide land-based mitigation services by storing carbon long-term in soil and wood. However, their mitigation potential has often been overlooked due to the lack of robust, context-specific estimates. This limits the development of targeted policies to support farmers involved in “carbon farming”—the use of agricultural practices to enhance CO₂ absorption. This study presents a model-based carbon accounting framework for assessing the climatic and economic benefits of agriculture-based mitigation in Mediterranean tree crop ecosystems. The approach does not rely on extensive field monitoring as its primary data source; however, it is calibrated and validated against targeted field measurements and experimental datasets generated within the LIFE CLIMATREE project, which constitute the validation basis of the analysis. The framework quantifies carbon removals and emissions under three management scenarios, ranging from business-as-usual practices to mitigation-rich management. Across representative Mediterranean countries and tree crops, mitigation-rich practices result in additional removals of approximately 1–2.5 t CO₂ ha⁻¹ yr⁻¹, with considerable variation across crop types and regions. These additional removals translate into meaningful economic values when assessed using indicative carbon prices, highlighting the potential contribution of tree crop management to climate action and agricultural sustainability. The findings support the development of carbon markets, eco-labeling, and agri-environmental schemes under the new Common Agricultural Policy. They also contribute to improving the accuracy of national GHG inventories in the LULUCF sector, which currently do not differentiate between orchard species or management practices. This evidence base is essential for shaping more effective climate policies and incentivizing sustainable land use.</p>