In the Mediterranean Region, species of the genus Juniperus face conservation challenges due to human activities and climate change threats. Juniperus species are reported to present low regeneration rate, while their seeds often exhibit physical and physiological dormancy. Viability and germination of mature Juniperus excelsa seeds from population originating from the Prespa area (Florina, Greece), alongside with seedling survival were investigated to study the reproduction dynamic of species population known to represent a EU priority habitat type of limited distribution and with low regeneration rate. The seed cut test of an uncleaned seed lot revealed a high percentage of empty seeds (90.03%) and a low embryo viability (2%). Cleaned seeds were subjected to a total of 44 pretreatments, categorised into eight groups targeting physical and physiological dormancy, along with combinations of these techniques. Despite most treatments showing limited success in enhancing germination, three pretreatments exhibited promising results (germination between 22.22% and 39.40%). Subsequent germination tests involving these treatments in controlled chambers, as well as in field conditions, along with hydration-dehydration cycles, were conducted using newly collected seeds. Seed germination rates in controlled chambers remained low, suggesting a deep primary dormancy. Pretreated seeds, under controlled field conditions, passed two winter periods fully saturated, with 13 hydrating-dehydrating cycles in-between. Germination was maximised during the second year of the field experiment, reaching almost 100% after mechanical scarification for 6 sec., followed by immersion in 3% H2O2 for 2 h. However, seedling survival was low, reaching approximately 38.26%. The findings emphasise the challenges in germinating Juniperus excelsa seeds and highlight the importance of the optimised protocols for reforestation in order to conserve this habitat type.