Abstract Background “Garra de Leon” (Leontochir ovallei) is an ephemeral endangered Alstroemeriaceae species endemic to Chile. Despite many efforts to improve the conservation of this species, the stimulation of dormant seeds and the production of rhizomes under controlled conditions remain unexplored. The aims of this study were to examine the germination responses of L. ovallei seeds under different in vitro conditions and to evaluate the formation of viable rhizomes after transplantation from in vitro to ex vitro conditions. Methods We evaluated five in vitro seed germination treatments: (1) acid scarification, (2) acid scarification followed by imbibition of seeds in aerated water, (3) imbibition of seeds in gibberellic acid, (4) clipping of seeds with a scalpel, and (5) seeds without any treatment (control). Seedlings obtained under in vitro conditions were transplanted to ex vitro conditions following a gradual acclimation process. After eight months, the number of rhizomes per plant was counted. To test asexual multiplication, each rhizome with its respective storage organ was divided using a scalpel and then left to rest for two years before subsequent evaluation of viability. After that period, the rhizomes were re-hydrated, and the emergence of plants after three months was evaluated. Results Seeds exposed to treatment 2 showed the highest germination percentage (36%), followed by the seeds whose coats were clipped (14%) and seeds treated with sulphuric acid (8%). The seed germination of the control treatment was 3%. After transplantation to ex vitro conditions, we obtained 220 rhizomes, with an average of three to six rhizomes per plant. After two years of dormancy, a total of 34 rhizomes (of 220 rhizomes) reactivated growth after re-ydration, indicating that, at least, 15,5% responded positively to watering. Conclusions We found that the seed germination of L. ovallei was increased by strong acidic conditions, suggesting that the main type of seed dormancy in this species is physical. However, germination was further increased by aeration, indicating embryo dormancy. In addition, we were able to obtain viable rhizomes by transplanting seedlings from in vitro to ex vitro conditions, which may be helpful for the propagation and ex situ conservation of this rare geophyte of Chile and potentially other geophyte species adapted to wet-dry cycle environments.