Seed recalcitrance is a major challenge in the conservation of many tropical species. Syzygium cuminii (L.) Skeels is a threatened species due to problems associated with natural regeneration and seed recalcitrance. The study was carried out to understand the physiology and biochemistry of jamun embryos during embryogeny and embryo desiccation. Maintenance of higher moisture content in the embryos was observed throughout embryogeny and lacked an embryo desiccation phase. Seeds germinated immediately after shedding without any dormant phase and desiccated very quickly and no other innate mechanisms in the seeds to prevent water loss. The critical threshold water level in the embryos was found to be 45% and a drop in water content significantly decreased the percentage of germination. The seeds remained viable for ten days and polyembryony was a frequent occurrence. FTIR analysis showed variations in biochemical composition during embryogeny and embryo desiccation. Embryo desiccation resulted in the lack of production of many biomolecules but induced the production of certain other compounds.