A patented strain of Bacillus amyloliquefaciens C-1 in our laboratory could produce functional sodium selenite (Na2SeO3) under optimized fermentation conditions. With the strong stress resistance and abundant secondary metabolites, C-1 showed potential to be developed as selenium-enriched postbiotics. C-1 has the ability to synthesize SeNPs when incubated with 100 μg/ml Na2SeO3 for 30 h at 30 °C aerobically with 10% seeds-culture. The transformation rate from Na2SeO3 into SeNPs reached to 55.51%. After selenium enrichment, there were no significant morphology changes in C-1 cells but obvious SeNPs accumulated inside of cells, observed by scanning electron microscope and transmission electron microscope, verified by energy dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy. SeNPs had antioxidant activity in radical scavenge of superoxide (O2−), Hydroxyl radical (OH−) and 1,1-diphenyl-2-picryl-hydrazine (DPPH), where scavenging ability of OH− is the highest. Selenium-enriched C-1 had obvious anti-inflammatory effect in protecting integrity of Caco-2 cell membrane destroyed by S. typhimurium; it could preventing inflammatory damage in Caco-2 stressed by 200 μM H2O2 for 4 h, with significantly reduced expression of IL-8 (1.687 vs. 3.487, P = 0.01), IL-1β (1.031 vs. 5.000, P < 0.001), TNF-α (2.677 vs. 9.331, P < 0.001), increased Claudin-1 (0.971 vs. 0.611, P < 0.001) and Occludin (0.750 vs. 0.307, P < 0.001). Transcriptome data analysis showed that there were 381 differential genes in the vegetative growth stage and 1674 differential genes in the sporulation stage of C-1 with and without selenium-enrichment. A total of 22 ABC transporter protein-related genes at vegetative stage and 70 ABC transporter protein-related genes at sporulation stage were founded. Genes encoding MsrA, thiol, glutathione and thioredoxin reduction were significantly up-regulated; genes related to ATP synthase such as atpA and atpD genes showed down-regulated during vegetative stage; the flagellar-related genes (flgG, fliM, fliL, and fliJ) showed down-regulated during sporulation stage. The motility, chemotaxis and colonization ability were weakened along with synthesized SeNPs accumulated intracellular at sporulation stage. B. amyloliquefaciens C-1 could convert extracellular selenite into intracellular SeNPs through the oxidation–reduction pathway, with strong selenium-enriched metabolism. The SeNPs and selenium-enriched cells had potential to be developed as nano-selenium biomaterials and selenium-enriched postbiotics.