This work was conducted over three-year monitoring seasons of three almond cultivars (Guara, Marta, and Lauranne) subjected to deficit irrigation in combination with cover crops in a Mediterranean semiarid area (SW, Spain). Four water–soil treatments were evaluated based on the conjunction of two irrigation strategies: fully irrigated (FI), covering 100% of the ETC, and regulated deficit irrigation (RDI), with two soil-management systems: bare soil (BS) and cover crop based on a mixture of vetch (Vicia sativa L.) and oat (Avena sativa L.) (CC). Throughout the study period in trees, the yield, the stem water potential (Ψstem), leaf nutrient content (N, P, K, Ca, Mg, Na, Fe, Zn, Mn, and Cu) in soils, organic carbon, microbial biomass, fluoresceine diacetate, and enzymatic activities (dehydrogenase, protease, β-glucosidase, and alkaline phosphatase) were determined. In addition, the dry matter and carbon fixation by plant covers were evaluated. For Guara and Lauranne, yield reductions (22 and 26%, respectively) were found for water-stressed (RDI-CC) plots with respect to non-stressed combination (FI-CC) plots, contrasting with cv. Marta, without a significant impact on productivity in all combinations. That is, the RDI (~3.000 m3 ha−1) strategy enabled acceptable productivity, offering promising possibilities for cultivation performance under water-scarcity scenarios. Important differences in Ψstem could be observed and ascribed to irrigation strategies, especially for Guara and Lauranne, but without significant effects due to the soil-management systems applied. No differences were observed in the tree nutritional status due to the presence or absence of CC; however, its presence increased the fixation of atmospheric carbon, which was not the case under BS conditions. Additionally, CC significantly fostered the microbial processes and enzymatic activities, particularly in upper soil layers (0–10 cm) and with plenty of water supply in FI-CC plots and to a lesser extent in RDI-CC plots, which could encourage prominent aspects for soil quality and health restoration. Thus, the cover crop is congruent with RDI to facilitate soil functionality and water savings in a changing climate, contributing to resilient farming systems in the Mediterranean environment.