Abscisic acid (ABA) plays an important role in the regulation of several stress responses such as drought, high salinity and low temperature being also proved as a key phytohormone for the acquisition of postharvest cold tolerance in zucchini fruit. Therefore, it would be of great interest to unravel the mechanisms implicated in the ABA response, using a metabolomic approach. The aim of this work has been to use a combination of metabolomic tools to identify the main metabolic pathways involved in ABA-mediated regulation of chilling tolerance in zucchini fruit. As a result of this study, it was found that ABA modulates the primary metabolism inducing the accumulation of some sugars, organic acids such as succinic acid and amino acids including histidine, serine, phenylalanine, glutamic acid and γ-aminobutyric acid, and that are involved in low-temperature tolerance. ABA treatment also activates the t-zeatin and riboflavin biosynthesis during the first days of cold storage which can be important signals in the ABA-mediated cold response to induce tolerance in zucchini fruit. Display omitted •Abscisic acid (ABA) improves postharvest quality of zucchini fruit.•Targeted metabolomics reveals an ABA modulation of the primary metabolism.•An accumulation of sugars, organic acids and amino acids induced chilling tolerance.•Secondary metabolism was also affected by ABA treatment.•ABA activates the t-zeatin and riboflavin biosynthesis at first day of cold stress.