[Objective] This study aimed to improve the organic selenium content of quinoa seeds and develop high-quality Se-rich quinoa food raw materials. [Methods] Using Qingbaili No. 1 quinoa as raw material and sodium selenite as a selenium source, the selenium-enriched germination process conditions of quinoa were optimized through one-way experiments combined with orthogonal experiments. The soluble protein, polyphenol content, and antioxidant capacity of selenium-enriched quinoa were further analyzed. [Results] The optimal process conditions for selenium-enriched germination of quinoa were sodium selenite solution concentration of 20 mg/L, soaking temperature of 25 ℃, soaking time of 6 h, soaking solution pH of 7.0, germination time of 48 h, and germination temperature of 20 ℃. Under these conditions, the organic selenium content of selenium-enriched germinated quinoa was 349.52 μg/kg. Selenium-enriched sprouted quinoa had the highest content of free phenols (236.35 mg/100 g) and bound phenols (198.31 mg/100 g), and control deionized water germinated quinoa had the highest content of soluble protein (22.18%). Notably, the antioxidant activities of soluble protein, free phenols, and bound phenols in selenium-rich germinated quinoa were the strongest, followed by those in control deionized water germinated quinoa, and untreated quinoa was relatively the lowest. [Conclusion] Se-enriched germination can significantly increase the contents of organic selenium, soluble protein and polyphenols, and enhance the antioxidant capacity of Quinoa.