BACKGROUND: Solid-state fermentation (SSF) is a general approach for preparing food and feed, which not only improves nutrition but also provides prebiotics and metabolites. Although many studies have been conducted on the effects of fermentation on feed substrate, the dynamics of microbiota and metabolites in SSF remain unclear. Here, high-throughput sequencing combined with gas chromatography-quadrupole time-of-flight mass spectrometry was used to evaluate the dynamic changes of solid fermented soybean meal and corn mixed matrix inoculated with Bacillus pumilus and Limosilactobacillus fermentum. RESULTS: Generally, inoculated bacteria rapidly proliferated, accompanied by the degradation of macromolecular proteins and an increase in the content of small peptides, trichloroacetic acid-soluble protein, free amino acids and organic acids. Bacillus, Lactobacillus and Enterococcus dominated the whole fermentation process. 389 non-volatile metabolites and 182 volatile metabolites were identified, including amino acids, organic acids, ketones, aldehydes, furans and pyrazine. Typical non-volatile metabolites such as lactic acid, 4-aminobutanoic acid, l-glutamic acid, d-arabinose and volatile metabolites such as 4-ethyl-2-methoxyphenol, 4-penten-2-ol, 2-pentanone, 2-ethylfuran, 2-methylhexanoic acid and butanoic acid-ethyl ester were significantly increased in two-stage solid fermentation. However, some adverse metabolites were also produced, such as oxalic acid, acetic acid, tyramine and n-butylamine, which may affect the quality of fermented feed. Sixteen genera were significantly correlated with differential non-volatile metabolites, while 11 genera were significantly correlated with differential volatile metabolites. CONCLUSION: These results characterized the dynamic changes in the process of two-stage solid-state fermentation with Bacillus pumilus and Limosilactobacillus fermentum and provided a potential reference for additional intervention on improving the effectiveness and efficiency of solid-state fermentation of feed in the future. © 2023 Society of Chemical Industry.