The prevalence of apples as the most widely consumed fruit globally does not exempt them from storage-related issues, resulting in substantial harvest losses. A prominent concern is the development of rot due to various factors during storage. This research endeavors to examine the influence of agrotechnological methods on the longevity of apples and the incidence of rot throughout storage. Apple trees (Malus domestica Borkh. cv. Rubin) grafted on dwarfing rootstocks P60 were planted in 2010 in single rows with a spacing of 1.25 m between trees and 3.5 m between rows. Eight combinations of different growth control measures (manual, mechanical pruning, spraying, trunk cutting) were selected for the experiment. The implementation of mechanical pruning, in conjunction with trunk cutting and Ca-prohexadione spraying, as well as summer pruning, detrimentally impacted the shelf life of apples. Examination of the storage period revealed a loss of 33–40% of the crop due to rot. Conversely, manual pruning sustained a consistent level of phenolic compounds throughout the storage period. Other pruning methods resulted in a notable increase in phenolic compounds, ranging from 67% to a two-fold rise compared to the compounds present at harvest. However, the integration of mechanical pruning with subsequent manual pruning not only significantly augmented the yield of apples but also yielded a shelf life akin to that of manually pruned apples. Following the analysis of the results, it is advisable to conduct mechanical pruning of the apples intended for storage along with supplementary manual pruning.