Mediterranean woody crops, such as olive and almond farming, and vineyards are usually cultivated in soils low in organic matter, with limited water availability and frequently on medium to steep slopes. Therefore, when conventionally cultivated, soils of these cropping systems are net sources of CO2 (throughout soil erosion and organic carbon mineralization). A promising option to sequester carbon (C) in these cropping systems is the implementation of recommended management practices (RMPs), which include plant cover in the inter-row area, minimum or no tillage and off- and on-farm organic matter amendments. However, the effects of RMPs on soil organic carbon (SOC) stocks in these cropping systems are widely overlooked, despite the critical importance of estimating their contribution on CO2 emissions for policy decisions in the agriculture sector in Mediterranean regions. We therefore conducted a meta-analysis to derive a C response ratio, soil C sequestration rate and soil C sequestration efficiency under RMPs, compared to conventional management of olive and almond orchards, and vineyards (144 data sets from 51 references). RMPs included organic amendments (OA), plant cover (CC) and a combination of the two (CMP). The highest soil C sequestration rate (5.3tCha−1 yr−1) was observed following the application OA in olive orchards (especially after olive mill pomace application), whereas CC management achieved the lowest C sequestration rates (1.1, 0.78 and 2.0tCha−1 yr−1, for olive orchards, vineyards and almond orchards, respectively). Efficiency of soil C sequestration was greater than 100% after OA and CMP managements, indicating that: i) some of the organic C inputs were unaccounted for, and ii) a positive feedback effect of the application of these amendments on SOC retention (e.g. reduction of soil erosion) and on protective mechanisms of the SOC which reduce CO2 emissions. Soil C sequestration rate tended to be highest during the first years after the change of the management and progressively decreased. Studies performed in Mediterranean sub-climates of low annual precipitation had lower values of soil C sequestration rate, likely due to a lower biomass production of the crop and other plant cover. Soil C sequestration rates in olive farming were much higher than that of vineyards, mainly due to the application of higher annual doses of organic amendments. The relatively high sequestration rate combined with the relative large spatial extent of these cropping system areas suggests that the adoption of RMPs is a sustainable and efficient measure to mitigate climate change.