The purpose of this study was to improve the protocol of clonal micropropagation for effective mass production of the Zarya Alatau apple cultivar through the use of axillary buds. In Kazakhstan’s challenging climate, the Zarya Alatau apple thrives because of its unique traits, including fruit preservation until May, cold hardiness, and resistance to scab and powdery mildew. Micropropagation is essential for healthy mother tree establishment, and this research focused on key factors for successful in vitro propagation. The sterilization of explants was optimized: 1.6% solution of sodium hypochlorite effectively sterilized plant materials for 10 minutes. Nutrient media composition was evaluated for efficient shoot regeneration. The study examined axillary bud regeneration on Murashige and Skoog medium with different concentrations of hormones. A combination of 6-benzylaminopurine (0.5 mg/L) and gibberellic acid (0.5 mg/L) yielded optimal results, with shoots reaching 3.5 cm. Root induction was analyzed with varying indole-3-acetic acid (IAA) concentrations, and the best results were achieved with 1.5 mg/L IAA, resulting in an 85% rooting frequency. Adapting in vitro plants to ex vitro conditions is crucial given their sensitivity to environmental changes. Well-developed leaves and a robust root system are essential for successful acclimatization during transplantation into a soil substrate. This research provides valuable insights into the critical parameters for a successful transition of in vitro propagated plants to soil conditions, optimizing micropropagation practices.