Effective selenium supplementation strategies are essential for alleviating global selenium deficiency. This study utilized the high‑selenium-tolerant strain Lactiplantibacillus plantarum NML21 to produce selenium-enriched yogurt, successfully converting inorganic Se(IV) into organic selenium, with selenoproteins accounting for 69.52 % of the total selenium content (995.19 ± 68.60 μg/g). Selenium-enriched yogurt exhibited excellent physicochemical properties and antioxidant activity. Volatile flavor analysis identified 36 compounds, with NML21 and SeNML21 significantly enhancing ketone flavors in yogurt, particularly increasing the contents of 2-heptanone and 2,3-pentanedione. Untargeted metabolomics identified 215 non-volatile metabolites, with NML21 and SeNML21 significantly regulating key metabolic pathways, including the phosphotransferase system, ABC transporters, and amino acid biosynthesis, promoting the accumulation of beneficial metabolites. Selenium specifically influenced the biosynthesis pathways of ABC transporters, phenylalanine, tyrosine, and tryptophan. This study demonstrates that NML21 is a promising strain for producing selenium-enriched functional yogurt, offering innovative perspectives for dietary selenium supplementation and functional food development.