<p>Bagging is a critical agronomic practice in apple cultivation that enhances fruit stress resistance, improves the proportion of high-quality fruit, and ensures overall fruit quality. However, recent studies have indicated that bagging may have a negative effect on some quality attributes of apples, but the underlying mechanism of action has not been fully elucidated. We hypothesize that mineral elements play a pivotal role in regulating these quality-related changes. In this study, we investigated the effects of mineral elements on the fruit quality of Fuji apples under both bagging and unbagging conditions. Results showed that bagging significantly increased the sugar-to-acid ratio in the apple peel while markedly reducing the contents of fructose, sorbitol, glucose, sucrose, and total anthocyanins in the fruit. The antioxidant capacity of the sarcocarp decreased progressively during storage, from high to low, after five days. Additionally, significant changes were observed in the levels of Cu, Mn, Zn, Fe, Mg, Ca, S, P, and K, which are closely associated with fruit quality. Correlation analysis revealed that pre-bagging peel nutrient elements were primarily linked to apple quality, whereas post-bagging correlations became more dispersed. Based on these findings, variations in nutrient element profiles represent a key factor influencing apple quality through bagging technology. Additionally, the adoption of bag-free cultivation methods seems more beneficial for improving the inherent quality and flavor characteristics of apples.</p>