The implementation of alley cropping in orchards can be a sustainable strategy to increase farm productivity by crop diversification and contribute to climate change mitigation. In this research, we evaluated the short-term effect of alley cropping with reduced tillage on soil CO2 and N2O emissions and soil total organic carbon (TOC) in an almond orchard under Mediterranean rainfed conditions. We compared an almond monoculture with tillage in all plot surface (MC) with almond crop with reduced tillage and growth of Capparis spinosa (D1) and almond crop with reduced tillage and growth of Thymus hyemalis (D2). For two years, soil CO2 and N2O were measured, with soil sampling at the start and end of the experimental period. Results showed that CO2 emission rates followed the soil temperature pattern, while N2O emissions were not correlated with temperature nor moisture. Soil CO2 emissions were significantly higher in MC (87 mg m-2 h-1), with no significant differences between D1 and D2 (69 mg m-2 h-1). Some peaks in CO2 effluxes were observed after tillage operations during warm days. Soil N2O emission rates were not significantly different among treatments. Cumulative CO2 and CO2 equivalent (CO2e) emissions were significantly highest in MC. When CO2e emissions were expressed on a crop production basis, D2 showed the significantly lowest values (5080 g kg-1) compared to D1 (50,419 g kg-1) and MC (87,836 g kg-1), owing to the high thyme yield, additional to the almond yield. No production was obtained for C. spinosa, since at least two more years are required. TOC did not change with time in MC neither D1, but it significantly increased in D2 from 3.85 g kg-1 in 2019 to 4.62 g kg-1 in 2021. Thus, alley cropping can contribute to increase the agroecosystem productivity and reduce CO2 emissions. However, it is necessary to grow evergreen alley crops such as thyme to obtain short-term increases in soil organic matter. Thus, to estimate increases in TOC with alley cropping, the plantation density and the period required by the crop to cover most of the surface are essential factors at planning the cropping strategy.