Abstract Bacillus velezensis is widely used for agricultural biocontrol, due to its ability to enhance plant growth while suppressing the growth of microbial pathogens. However, there are few reports on its application in fermented feed. Here, a two-stage solid-state fermentation process using Bacillus velezensis followed by Lactobacillus plantarum was developed to degrade antinutritional factors (ANFs) and improve soybean meal (SBM) nutrition for animal feed. The process was evaluated for performance in degrading SBM antinutritional factors, dynamic changes in physicochemical characteristics, microorganisms and metabolites. After two-stage fermentation, degradation rates of glycinin and β-conglycinin contents reached 78.60% and 72.89%, respectively. The pH of fermented SBM (FSBM) decreased to 4.78 ± 0.04 and lactic acid content reached 183.38 ± 4.86 mmol/kg. NSP-degrading enzymes (Non-starch polysaccharide, NSPases) and protease were detected from the fermented product, which caused the changed microstructure of SBM. Compared to uninoculated SBM, FSBM exhibited increased proportions of crude protein (51.97 ± 0.44% vs. 47.28 ± 0.34%), Ca, total phosphorus (P), and trichloroacetic acid-soluble protein (11.79 ± 0.13% vs. 5.07 ± 0.06%). Additionally, cellulose and hemicellulose proportions declined by 22.10% and 39.15%, respectively. Total amino acid content increased by 5.05%, while the difference of AA content between the 24 h, 48 h and 72 h of fermentation was not significant (P > 0.05). Furthermore, FSBM also showed antibacterial activity against Staphylococcus aureus and Escherichia coli. These results demonstrated that two-stage SBM fermentation process based on Bacillus velezensis 157 and Lactobacillus plantarum BLCC2-0015 is an effective approach to reduce ANFs content and improve the quality of SBM feed.