Peels of Citrus unshiu contain abundant quantities of flavonoids, such as hesperidin and naringin. However, the factors affecting the quantity of flavonoids in those peels are still unidentified. This study focused on the effects of seasonal change and cultivation methods on the quantity of flavonoids in the peels of Citrus unshiu. Two cultivars of Citrus unshiu, Okitsu Wase and Aoshima unshiu, were harvested monthly at 3 different fields, from July 2022 to November 2022. The quantities of hesperidin, naringin, nobiletin, and tangeretin contained in the peels were compared by the field management; natural, conventional, and exemplary cultivation. Natural cultivation produced Citrus unshiu without the use of any agricultural chemicals and its field was covered with weeds, whereas other 2 fields use agricultural chemicals, and the fields were without any weeds. The quantities of those flavonoids in the peels of Okitsu Wase tend to decrease from July to November. Okitsu Wase, grown in natural cultivation contained the most quantities of four flavonoids compared to other Okitsu Wase grown in different fields. The results indicate that some levels of biotic or abiotic stress could promote the production of some types of flavonoids.