1-Deoxynojirimycin (DNJ) is an efficient alpha-glucosidase inhibitor (alpha-GI) with potential applications in the prevention and treatment of diabetes. In this study, 16 Bacillus strains were screened for alpha-GI rate, and the strain HZ-12 with the highest alpha-GI rate was identified as Bacillus amyloliquefaciens through the analysis of physiological biochemical characteristics and 16S rDNA sequence. By LC-MS/Q-TOF analysis, the alpha-GI component produced by B. amyloliquefaciens HZ-12 was identified as DNJ. Soybean was used as the substrate for the solid-state fermentation; 870 mg/kg DNJ was produced by B. amyloliquefaciens HZ-12 after optimizing the fermentation conditions and media, which was 3.83-fold higher than the initial yield. Also, evaluations of nutraceutical enrichment in the form of anticoagulant activity, antioxidant activity, total nitrogen (TN), and total reducing sugars (TRS) of the B. amyloliquefaciens HZ-12 fermented soybeans were substantially higher than unfermented soybeans. This study provided a promising strain for high-level production of DNJ and produced nutraceutical enriched soybeans by fermentation.