Sourdough flavors were closely related to microbial metabolism. The microbial diversity of foxtail millet dough during fermentation has never been studied. Here, the metabolic potential and diversity of the bacterial community were analyzed by metagenomic during dough fermentation. Firmicutes was the dominant phylum in the dough, within heterofermentative lactic acid bacteria (e.g., Companilactobacillus, Limosilactobacillus, Pediococcus and Lactobacillus) as the most abundant bacteria. Proteobacteria was gradually inhibited after fermentation. Companilactobacillus_crustorum was notably found abundant during dough leavening. Limosilactobacillus_fermentum increased markedly during fermentation, while Companilactobacillus_crustorum decreased significantly. For further exploration, genes associated with metabolism were annotated through metagenomics. Limosilactobacillus, Companilactobacillus and Pediococcus were actively engaged in glycolysis (ko00010), starch and sucrose metabolism (ko00500), and pyruvate metabolism (ko00620), leading in part to lactic and acetic acid accumulations and dough acidification. Limosilactobacillus and Lactiplantibacillus were the main contributors to key aminopeptidases or/and transaminases involved in amino acid metabolism, which was responsible for flavor metabolite formation. This study will provide an enhanced understanding of the predominance and diversity of dough bacterial communities, and contribute to future strain screening in the dough for better flavor.