A comparative study of fresh extra early ‘VioWhite 5’ nectarines, cultivated under long-term regulated deficit irrigation (RDI) strategies and stored under cold conditions, combined or not with a controlled atmosphere (CA; 3–4kPa O2 and 12–14kPa CO2) or 1-methylcyclopropene (1-MCP; 1.25μLL−1, 24h, 0°C), was performed. These strategies were: (i) non-deficit-irrigation (NDI), irrigated at 110% of maximum crop evapotranspiration (ETC) during the whole season; (ii) RDI1, irrigated at 110% ETc during critical periods of growth and at 85% of NDI during the rest of the growing season; (iii) RDI2, irrigated at 110% ETc during critical periods of growth and at 80 and 60% NDI during the second fruit growth stage in March and late postharvest, respectively. Quality factors and biochemical parameters were monitored. In general, RDI2 reached higher sensory evaluation scores mainly due to the higher soluble solids content. Weight loss was higher in air-stored nectarines with faster changes in firmness and color. The combination of cold storage with CA or 1-MCP better maintained the initial content of bioactive compounds. This fact highly correlated with soluble phenolic content, showing the involvement of phenolic compounds in the antioxidant activity of nectarines. A correlation between dehydroascorbic acid (DHA) concentration and stress were also found, resulting in the ability of using DHA concentration as a stress biomarker. The cultivation of extra early nectarines under RDI2 combined with the 1-MCP postharvest treatment was the best method for improving and maintaining overall quality while saving a notable amount of water (2050m3/ha and year).