To further improve the utilization rate of starch in the fermentation of Baoning vinegar, the effects of Aspergillus niger biofortification on the quality and microbial community of vinegar Pei (a mixture of fermentation materials) and Baoning vinegar were evaluated. The results suggested that the total acid content, a crucial parameter for vinegar production, in vinegar Pei increased by approximately 1.70 g/100 g at the end of fermentation. The utilization rate of starch and content of organic acid increased significantly after biofortification, and the content of lactic acid was the highest in Baoning vinegar, followed by acetic acid. Similarly, the total amount of free amino acids increased after biofortification, especially the content of histidine and tyrosine. The esters and acid compounds were the most abundant in the vinegar Pei, while the contents of acid and carbonyl compounds were the highest in liquid vinegar. As revealed by high-throughput sequencing, the microbial community in vinegar Pei changed little after biofortification. Lactic acid bacteria and yeast are the most abundant microbes throughout the fermentation process. The present study provides insights into the improvement of the solid-state brewing process of vinegar. •A. niger increased the usage of starch and total acid content in vinegar Pei.•A. niger increased the amino acid content, but maintained the flavor characteristics.•The microbial community changed little in vinegar Pei after biofortification.