The effect of long-term regulated deficit irrigation (RDI) strategies on bioactive compounds and enzymes at harvest, during cold storage [0 °C, 90% to 95% relative humidity (RH)] and after a simulated retail sale period (15 °C, 70% to 75% RH) of extra-early nectarine ‘VioWhite 5’ [Prunus persica (L.) Batsch] was evaluated for 3 consecutive years. RDI strategies were scheduled as follows: 1) control [irrigated at 110% of maximum crop evapotranspiration (ETc) during the whole season], 2) RDI1 (irrigated at 110% ETc during critical periods of growth and at 85% of control during the rest of the growing season), and 3) RDI2 (irrigated at 110% ETc during critical periods of growth and at 80% and 60% control during the second fruit growth stage in March and late postharvest, respectively). Results suggested the existence of water stress when RDI was applied on extra-early nectarine. The RDI effect induced a change on the activity of enzymes studied that depended on the intensity and duration of water stress. RDI fruit, especially RDI2, presented higher catalase (CAT), phenylalanine ammonia-lyase (PAL), and ascorbate peroxidase (APX) enzyme activity and, together with dehydroascorbic acid level, appeared as indicators of this abiotic stress. RDI nectarine fruit increased total phenolic and flavonoids contents improving the nutraceutical quality of the product. With storage, polyphenol oxidase (PPO) increased its activity through the reduction of flavonoids, particularly in pulp. In this study, RDI2 achieved the highest initial and stored antioxidant capacity values. Peel compared with pulp was the main tissue where bioactive compounds were found in ‘VioWhite 5’ nectarine fruit and the only tissue with anthocyanin content in this white pulp nectarine. The significant water savings were of 780 and 2050 m3·ha−1 per year for RDI1 and RDI2, respectively. RDI can be used as a field practice to enhance bioactive compounds on extra-early nectarine fruit and to contribute to reduce water demand.