Somatic embryogenesis is a useful method for propagating selected plant material. However, before using this technique for forest tree deployment, it is important to ensure high-quality somatic embryos (SEs). This quality depends on how closely SEs resemble zygotic embryos (ZEs). At the end of their maturation, SEs usually resemble ZEs from fresh seeds due to their high water content and biochemical composition. For this reason, an effective desiccation method is needed to lower the SEs’ water content to levels similar to fully mature dry ZEs, while ensuring a high percentage of germination and successful conversion into plants. To establish an efficient desiccation protocol, we investigated the biological, histological, biochemical and molecular changes in the SEs of hybrid larch Larix eurolepis exposed to desiccation at high relative humidity (RH; 98%), reduced RH (59%), or a combination of both. For the first time in conifers, we have demonstrated the possibility of obtaining desiccated SEs with reduced water content similar to dry ZEs while maintaining a high rate of germination and conversion into plants. This treatment could also be considered as a potential method for SE storage. This multi-scale study contributes significantly to the knowledge on desiccation of conifer SEs.