This study aimed to evaluate the physiological changes in pindo palm (Butia capitata) seeds, a native fruit species of the Brazilian Cerrado, over time under different storage conditions. Pyrenes (endocarp+seed) were stored on the sand under shade and refrigeration conditions. The physiological quality of seeds and embryos (via in vitro culture) was evaluated over time. Moisture content decreased during storage until stabilization, while germination, germination speed index (GSI), and operculum resistance remained stable up to 90 days, with a significant decline at 120 and 150 days. Conversely, lipid peroxidation, measured by malondialdehyde (MDA) content, and electrical conductivity (EC) increased over time, especially after 90 days. Refrigeration promoted greater embryo elongation, but sheath and root emergence were reduced. Storage reduces seed dormancy in B. capitata but also decreases viability and vigor.