Abstract Purpose Diversification practices such as intercropping in woody cropping systems have recently been proposed as a promising management strategy for addressing problems related to soil degradation, climate change mitigation and food security. In this study, we assess the impact of several diversification practices in different management regimes on the main carbon fluxes regulating the soil carbon balance under semiarid Mediterranean conditions. Methods The study was conducted in two nearby cropping systems: (i) a low input rainfed almond (Prunus dulcis Mill.) orchard cultivated on terraces and (ii) a levelled intensively irrigated mandarin (Citrus reticulata Blanco) orchard with a street-ridge morphology. The almond trees were intercropped with Capparis spinosa or with Thymus hyemalis While the mandarin trees were intercropped with a mixture of barley and vetch followed by fava bean. Changes caused by crop diversifications on C inputs into the soil and C outputs from the soil were estimated. Results Crop diversification did not affect soil organic carbon stocks but did affect the carbon inputs and outputs regulating the soil carbon balance of above Mediterranean agroecosystems. Crop diversification with perennials in the low-input rainfed woody crop system significantly improved the annual soil C balance in the short-term. However, crop diversification with annual species in the intensively managed woody crop system had not effect on the annual soil C balance. Conclusions Our results highlight the potential of intercropping with perennials in rainfed woody crop systems for climate change mitigation through soil carbon sequestration.