We previously found that glucagon-like peptide 1 (GLP-1) secretion by co-administration of maltose plus an α-glucosidase inhibitor miglitol (maltose/miglitol) was suppressed by a GLUT2 inhibitor phloretin in mice. In addition, maltose/miglitol inhibited glucose-dependent insulinotropic polypeptide (GIP) secretion through a mechanism involving short chain fatty acids (SCFAs) produced by microbiome. However, it remains unknown whether phloretin suppresses GLP-1 secretion by modulating SCFAs. In this study, we examined the effect of phloretin on SCFA release from microbiome in vitro and in vivo. In Escherichia coli, acetate release into the medium was suppressed by phloretin, when cultured with maltose/miglitol. In mice, phloretin inhibited maltose/miglitol-induced SCFA increase in the portal vein. In addition, alpha methyl-d-glucose (αMDG), a poor substrate for GLUT2, significantly increased GLP-1 secretion when co-administered with phloridzin in mice, suggesting that GLUT2 is not essential for glucose/phloridzin-induced GLP-1 secretion. αMDG increased portal SCFA levels, thereby increasing GLP-1 secretion and suppressing GIP secretion in mice, suggesting that αMDG is metabolizable not for mammals, but for microbiota. In conclusion, phloretin is suggested to suppress maltose/miglitol-induced GLP-1 secretion via inhibiting SCFAs produced by microbiome.