Hot and dry Mediterranean ecoregions are characterized by low soil organic carbon content and large potential to become carbon sink when appropriately managed. Soil carbon sequestration may also play an important role in improving the resilience of these vulnerable agroecosystems to increasingly drastic impacts of global climate change. One agricultural practice that aims to increase soil organic carbon stocks, among other beneficial outcomes, is the use of cover crops. Although cover crops can increase soil organic carbon content, recent studies have observed that cover crops may lead to lower soil carbon stocks when considering co-management strategies, especially at greater soil depths. In this review, we outline the current paradigm of soil organic carbon dynamics and aim to apply our current understanding of soil carbon sequestration processes to cover crop management. We review how cover crop practices such as cover crop species selection, growth duration, and termination methodologies may impact soil organic matter sequestration and stabilization processes and provide insights to direct future research and inform cover crop management for C sequestration in Mediterranean agroecosystems.