Fresh-cut ‘Big Top’ nectarines were dipped in 2% (w/v) ascorbic acid–1% (w/v) calcium lactate and stored at 4 °C for up to 12 days in 10 kPa O2- and 10 kPa CO2-modified atmosphere packaging (MAP). The used microperforated plastic film allowed O2 and CO2 concentrations to reach steady values from the fifth day in storage onwards. Samples stored in MAP after chemical dipping showed the highest visual quality score, slight browning symptoms, increment in firmness and very low ethanol and acetaldehyde content. The chemical dipping also increased antioxidant capacity, probably due to the effect of ascorbic acid. The results suggested that the control of yeasts was mainly exerted by MAP, whereas only a slight effect was achieved by the chemical dipping. Therefore, MAP plus ascorbic acid/calcium lactate dipping was the best combination to preserve phytochemical content, antioxidant capacity and microbiological safety of fresh-cut nectarines during storage.