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The deforestation and degradation of natural habitats is the second largest contributor to carbon dioxide (CO2) emissions to the atmosphere. Temperate forests cover similar to 16.5% of the Mexican landscape, and are a priority ecosystem for global conservation due to their high rate of endemism and species diversity. These forests also provide valuable ecosystem services, including the storage of organic carbon. Mexican temperate forests have lost more than half of their original cover, with ongoing forest degradation, resulting in CO2 emissions to the atmosphere. Most studies and carbon inventories only consider organic carbon stored in the aboveground biomass, and do not consider the organic carbon stored within soils of temperate forests. As a result, the emissions of CO2 due to deforestation are underestimated, and the value of temperate forests is underappreciated. To address this shortcoming, (1) we examine the extent and factors determining soil organic carbon stocks; (2) we estimate soil organic carbon stocks of Mexican temperate forests, the CO2 emissions caused by deforestation and avoided emissions from conservation and (3) we discuss the causes of loss of soil OC and management strategies to mitigate this loss. We propose that including the soil organic carbon stock-component is a priority for national projects targeting reducing emissions from deforestation. Also, urgent studies on the impacts of forest degradation in stocks of soil organic carbon are needed. Management strategies for conservation and rehabilitation of Mexican temperate forests must consider social and economic aspects of the local communities.