The sustainability of woody crop agroecosystems requires continued improvements to water, nutrient and soil management. In this work, the combination of resource availability or fertigation dose with soil management practices was tested in a 2 × 2 factorial design in a drip irrigated young almond orchard. The fertigation doses were: the farmer supply at 60% of crop evapotranspiration and full nutrient requirements and the half-farmer supply at 30% of crop evapotranspiration and half nutrient requirements. The soil management practices were: bare soil and cover crops in the inter-row (mixture of grasses and legumes). Tree growth, yield, water and nutrient status, and cover crop biomass and nutrient status were determined, as well as inter-row soil C and N concentration. Results showed that the effect of resource availability was independent of soil management and vice versa. The half farmer treatment reduced tree vegetative growth and yield compared to farmer treatment, due to a negative effect on the water status, without observing a decrease in the concentration of nutrients in leaves or fruit. Trees with cover crop also reduced growth and yield compared to bare soil management. This was due to a nutritional competition, mainly of Ca, Fe, Mn and Zn, rather than to a decline in tree water status. Cover crops sequester up to 1 t/ha/year of carbon but do not increase soil organic carbon, nor soil total nitrogen. Cover crops proved to be efficient in reducing soil nitrate concentration in the topsoil and therefore has potential to prevent its leaching. Deficit fertigation and the use of cover crops can be effective practices to preserve and save water and nutrient resources in Mediterranean agroecosystems, but should be established with caution so as not to compromise the profitability of the orchard.