The conservation of biodiversity requires efficient ex situ methods for the storage of plant genetic material outside the natural habitat. This approach allows for the preservation of valuable, endemic, and endangered plant species for a long time. One widely used method is medium-term storage in in vitro culture. In our work, we describe the results of medium-term storage of microclonally propagated shoots of an endangered and endemic species of the Malus niedzwetzkyana. In vitro preservation was realized with the help of osmotic agents in the nutrient medium. For this, there were studied the cultivation conditions such as temperature (4°C and 24°C) and photoperiod (16/8 and growing in the dark), and the composition of nutrient media to slow growth (sucrose, mannitol, PVP, abscisic acid). The research results showed that the optimal condition for medium-term storage of shoots is the QL nutrient medium with the addition of 3% or 6% sucrose under standard conditions (24°C, photoperiod 16/8). The optimized protocol made it possible to preserve Malus niedzwetzkyana explants for 2 months without recultivation. Moreover, the stage of explant recovery was fast, during only one passage.