Nectarine [Prunus persica (L.) Batsch] is a sought-after fruit due to its properties. In addition, minimally processed produces are more and more accepted by consumers. Four nectarine cultivars (‘Early Top’, ‘Nectaprima’, ‘Big Top’ and ‘Venus’) were selected to study their suitability for minimal processing. Samples were processed in a clean room at 8 °C, washed them in water (4 °C) and stored at 4 °C in modified atmosphere packaging. The samples were analysed at 0, 3, 6 and 9 days of storage, and quality parameters as well as functional compounds (polyphenols and polyphenol oxidase activity) were studied. Principal component analysis (PCA) was carried out to assess the relationship between nectarine cultivars and determined parameters. In conclusion, ‘Early Top’ and ‘Nectaprima’ cultivars showed the best quality results and therefore a promising suitability for fresh-cut processing. Nevertheless, the remaining cultivars should not be ruled out due to their functional content, advising additional conservation treatments for them.