While foxtail millet boasts high nutritional value, its use is still not fully realized. Various fermentation agents were used on millet dough to enhance the flavor and quality of staple foods based on millet. The study investigates the effects of fermentation on the gelatinization properties, rheological behavior, water distribution, microstructure, and flavor profile of foxtail millet steamed bread. Results showed an increase in the viscosity of sourdough millet dough (SD) and lactic acid bacteria millet dough (LABD) compared to the yeast millet dough, indicating enhanced stability of the products when multiple microbial strains were added. In the LABD, lactic acid bacteria metabolism reduced hydrogen atom levels, shortened peak time, and improved water retention. The tanδ initially decreased and then stabilized as angular frequency increased, demonstrating higher viscoelasticity and better maintenance of the gluten network. Microstructural analysis revealed that natural fermentation enhanced the gluten network in the dough through enzymatic modification of protein structures. SD and LABD fermentation significantly improved the texture of the steamed bread and enhanced the aroma of volatile compounds, particularly esters and aldehydes. Ethyl lactate and ethyl nonanoate were identified as potential contributors to the natural and fresh aroma of the bread. These findings indicate that multi-strain natural fermentation is valuable in practical applications and may inspire future innovations in millet-based staple food production.