In recent years, interest in Lonicera caerulea production has grown significantly because of its nutritional and pharmaceutical benefits, leading to rapid expansion in its cultivation. L caerulea var. emphyllocalyx is a lesser-known botanical variety. Due to differences between plants of the Lonicera genus and the lack of scientific reports on micropropagation, it is necessary to determine the possibilities of in vitro propagation. The aim of this study was to elaborate a micropropagation protocol of two new breeding clones of Lonicera caerulea var. emphyllocalyx: ‘21–17’ and ‘139–24’. The experiments were carried out on in vitro cultures grown on MS medium supplemented with 1 mg·dm−3 BA or 1 mg·dm−3 mT. Two types of explants were used during the experiment: nodal fragments (NFs) and shoot-tips (STs). Before acclimatisation, some rooted microshoots were subjected to cooling at 4 °C for 4 weeks. Significantly more ST explants than NF explants started to grow at the proliferation stage. The application of BA resulted in much better proliferation and health of cultures. Cold storage of micropropagated ‘139–24’ plantlets significantly increased their survival in acclimatisation in contrast to ‘21–17’ plantlets but weakened further growth of the plants. In future in vitro studies on L. caerulea var. emphyllocalyx, BA can be used as the primary growth regulator due to its effectiveness and low cost. Nodal fragments should be considered as the main propagation material since they promote better growth rates. Additionally, further research is required to explore the effects of low-temperature storage on the growth and physiology of these plants. The results obtained in this research may contribute to the development of micropropagation technology in the future for L. caerulea var. emphyllocalyx.