• Metabolomic markers of chilling injury were identified across zucchini cultivars. • Polyphenol accumulation contributed to improved fruit quality during cold storage. • Amino acids, nucleotides and phytohormones supported postharvest cold tolerance. • Tocopherol and pyridoxal enhanced antioxidant protection during cold storage. • The tolerant inbred line 4.7 accumulated cucurbitacins B and I under cold conditions. Zucchini (Cucurbita pepo L.) is highly sensitive to chilling injury during cold