The effect of high-temperature-conditioning treatments (1–2days at 37°C) on fruit quality, flavonoids, total antioxidant capacity (TAC) and vitamin C was investigated in chilling-sensitive ‘Fortune’ mandarins subjected to single or double quarantine treatments (16 or 32days at 1.5°C, respectively). High temperature-conditioning treatments, which reduced chilling injury, allowed fruits to withstand quarantine treatments without affecting the fruit quality, vitamin C or TAC. Hesperidin and isorhoifolin were the most abundant flavonoids followed by didymin and narirutin, whereas the polymethoxylated flavones (PMFs) nobiletin and tangeretin were the less abundants. Didymin and narirutin slightly increased (∼1.5-fold) at 1.5°C. A 4-fold increase occurred in eriocitrin, though its concentration was much lower. Small differences in flavonoids were found between non-conditioned fruit and fruit conditioned for 1day after cold storage and their concentration in carpellary membranes were, in general, much higher than in juice. Therefore, fruit conditioning at 37°C allows chilling-sensitive citrus cultivars to withstand quarantine treatments without having deleterious effects on the fruit quality, vitamin C or relevant flavonoids.