Citrus fruits have a distinctive flavor and can convey health benefits because of their unique phytochemicals. Phytochemical profiles are influenced by many factors, including variety and environmental growing conditions; however, the effect of the cultivation methods on the phytochemical profile of Satsuma mandarin (Citrus unshiu) has received little attention. In this study, we examined the relationships between the cultivation conditions, sensory quality, and phytochemical profiles of C. unshiu cultivated using four methods: open field, greenhouse, film mulching, and tunnel farming. The soil water content differed significantly between the cultivation methods and showed a strong positive correlation with sourness, bitterness, and astringency and a strong negative correlation with sweetness. The metabolites of C. unshiu were not associated with the soil water content but with the soil mineral content, including nitrogen (N+), phosphorus (P+), and potassium (K+). The soil P+ and K+ content was positively correlated with most secondary metabolites. The relative abundance of sugars did not differ significantly between the cultivation methods; however, the sweetness was higher under film mulching than under the other cultivation methods because of the suppression of sweetness by bitter compounds. We did not investigate the effect of other growing conditions, such as sunlight; however, the results improve our understanding of the effect of cultivation methods on the quality of C. unshiu and may inform crucial decisions concerning citrus cultivation.