Peach is the third most important temperate fruit crop considering fruit production and harvested area in the world. Exporting peaches represents a challenge due to the long-distance export markets. This requires fruit to be placed in cold storage for a long time, which can induce a physiological disorder known as chilling injury (CI). The main symptom of CI is mealiness which is perceived as non-juicy fruit by consumers. The purpose of this work was to identify and compare the metabolic and lipid profile between two siblings from a contrasting population for juice content, at harvest and after 30 days at 0°C. A total of 119 metabolites and 189 lipids were identified, which showed significant differences of abundance including mainly in amino acids, sugars and lipids. Our results indicate that some of the top metabolites and lipids could be used as biomarkers associated with mealiness at harvest and after cold storage.