Se-enriched Lactobacillus bulgaricus (L. bulgaricus) was generated by administration of sodium selenite (0, 1, 4, 8, 16, 32, and 64 mg/L, respectively) in MRS medium and enriched selenium manifestation in L. bulgaricus was investigated using transmission electron microscopy and energy-dispersive X-ray spectrometry and alterations of essential elements and amino acids in the organism were evaluated. We demonstrate that administration of sodium selenite in the dosage of 1-16 mg/L is suitable for selenium enrichment in L. bulgaricus and can enhance nutritive value in the organism by elevating the contents of essential elements including P, Mg, Mn, Zn, Ca, and total amino acids as well as reducing selenite to insoluble elemental selenium, an electron-dense and amorphous Se (0) granule, thereby depositing it both in the cytoplasm and in the extracellular space of L. bulgaricus. Thus, Se-enriched Lactobacillus can provide a potential dietary source of nontoxic selenium and functional regulator used for food and medical industry.