This study focused on improving the flavor quality of seasonings, and enzymatic hydrolysis of soybean protein isolate (SPI) seasoning via traditional technology may lead to undesirable flavors. Herein, we aimed to develop a new type of SPI seasoning through microbial fermentation to improve its flavor quality. The effect of Corynebacterium glutamicum fermentation on the flavoring compounds of seasonings in SPI enzymatic hydrolysate was examined. Sensory evaluation showed that the SPI seasoning had mainly aromatic and roasted flavor, and the response signals of S18 (aromatic compounds), S24 (alcohols and aldehydes), and S25 (esters and ketones) sensors of the electronic nose differed significantly. Overall, 91 volatile compounds were identified via gas chromatography–mass spectrometry. SPI seasonings contained a higher number of alcohols, ketones, aromatics, and heterocyclic compounds than traditional seasonings, which had stronger cheese, fatty, and roasted aromas. According to the relative odor activity value (ROAV) analysis, n-pentylpyrzine, 2,6-dimethylpyrazine, and tetramethylpyrazine are the key flavoring compounds (ROAV ≥ 1) of SPI seasoning, which may impart a unique roasted and meaty aroma. Therefore, the fermentation of SPI enzymatic hydrolysate with C. glutamicum may improve the flavor quality of its products, providing a new method for the development and production of new seasoning products.