Cinchona officinalis has experienced anthropogenic pressures for nearly 400 years, such as overexploitation, habitat fragmentation, and the subsequent reduction of genetic diversity. Additionally, the challenge of regeneration in its natural environment makes it a vulnerable species. In this context, various treatments for the in vitro conservation of explants were evaluated in the present study. For short-term conservation, the effects of osmotic substances such as sorbitol, mannitol, and sucrose at different concentrations were assessed. Different concentrations of MS and B5 culture media were also examined for their impact on the growth, budding, mortality, and rooting of explants over 12 months without subcultures. For long-term conservation by cryopreservation, two techniques were tested: vitrification and encapsulation-dehydration. Short-term preservation of explants in sorbitol resulted in low mortality, minimal growth, and limited development of new shoots compared to preservation in sucrose or mannitol, although tissues could be recovered successfully from all storage conditions. After cryopreservation and 45 days of recovery, explants with the lowest mortality (4%) were from the control treatment, cultivated in a medium with sucrose which proved useful as a cryoprotectant, followed by the encapsulation-dehydration treatment. In conclusion, it is possible to conserve C. officinalis tissues in the short-term using in vitro techniques, while further assays are needed for long-term conservation.