Almond (Prunus dulcis Mill. [D.A. Webb]) is the third most widely spread crop in Spain and has traditionally been cultivated in marginal areas and shallow soils under rainfed conditions. However, it recently has been progressively introduced in flat irrigated areas. The implementation of cover crops in the inter-rows of woody crops has been proven as a suitable strategy to reduce the runoff and soil erosion but they also can boost soil quality and health. A field experiment was conducted during two-monitoring seasons to examine the soil nitrogen and carbon sequestration potential of three seeded cover crops [barley (Hordeum vulgare L.), hairy vetch (Vicia villosa Roth), and a mixture of 65% barley and 35% vetch] and a control of spontaneous flora in irrigated almond orchards (SW Spain). Here, we show that barley provided the highest biomass amount, followed by mixture covers, vetch, and the control treatment. Also, vetch covered the soil faster in the growing stage, but its residues were decomposed easier than barley and mixture treatments during the decomposition period after mowing, providing less soil protection when the risk of water erosion with autumn rainfall is high. On the other hand, vetch improved soil nitrate content by over 35% with respect to barley and mixture treatments at 0–20 cm soil depth throughout the studied period. In addition, a greater carbon input to the soil was determined in the barley plot. That is, the mixture and barley cover crops had higher potential for carbon sequestration, augmenting the soil organic carbon by more than 1.0 Mg ha−1 during the study period. Thus, taking into consideration the findings of the present experiment, the establishment of a seeded cover crop would be more advisable than spontaneous flora to mitigate soil erosion, enhancing soil fertility and carbon sequestration in irrigated almond plantations in Mediterranean semi-arid regions.