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• Lactobacillus , Acetobacter , Bacillus , Clostridium and Weissella were the dominant bacteria in naturally fermented acidic gruel. • There were covariability between bacterial community and sensory quality. • Bacterial gene function was mainly related to transport and metabolism of amino acids and carbohydrates. • Concentrations of amino acids, organic acids and soluble solids in Guangxi acidic gruel were higher than in Shanxi and Inner Mongolia. Acidic gruel is a popular and nutritious fermented cereal food in China. However, the relationship between microbial function and quality of traditionally-fermented acidic gruel has not been evaluated. In this study, the microbiome, sensory quality and nutritional components of 98 samples of naturally fermented acidic gruel collected from Guangxi, Shanxi and Inner Mongolia were analyzed by high-throughput sequencing combined with various determination methods. High-throughput sequencing showed bacteria in acidic gruel belonged mainly to the genera Lactobacillus , Acetobacter , Bacillus , Clostridium and Weissella. Bacterial community composition and sensory quality of samples from Shanxi and Inner Mongolia were similar, but significantly different from Guangxi samples (p < 0.05). PICRUSt showed that gene functions were mostly related to carbohydrate and amino acid metabolism; all dominant bacterial genera, except Lactobacillus , were related to taste and volatile flavour indices. Acidic gruel was rich in amino acids, organic acids and soluble solids, which were in significantly higher concentrations in samples from Guangxi than in samples from Shanxi and Inner Mongolia; pH values of samples from Guangxi were also the highest. These differences may be caused by geographical, environmental or manufacturing differences. [ABSTRACT FROM AUTHOR]