The present investigation evaluated the impact of pruning on yield, fruit quality, leaf nutrient composition and disease incidence in mango cv. Amrapali. Pruning significantly influenced fruit weight, yield dynamics, biochemical quality attributes, leaf nutritional status and disease infestation. Although fruit yield of pruned trees declined during the first year following pruning compared with that of unpruned trees, a marked increase was recorded in the subsequent year, indicating a strong compensatory response. Leaf nutrient analysis revealed greater concentrations of K, Mg, S, Cu, Zn and Mn in pruned trees, whereas N, P, Ca and Fe concentrations were higher in unpruned trees. Pruning also noticeably decreased the incidence of major diseases, including anthracnose and stem-end rot in fruits and anthracnose and red rust in leaves. Strong positive correlations were observed among ascorbic acid, carotenoids, antioxidant activity, and total phenolic content (r = 0.87–0.99). The beneficial effects of pruning were attributed to improved light penetration, enhanced air circulation, stimulation of new vegetative growth and more efficient nutrient redistribution. This study demonstrates that strategic pruning improves fruit nutritional quality, plant health and long-term productivity in mango cv. Amrapali, highlighting the importance of regular and judicious pruning for sustainable mango orchard management.