ObjectiveThe study aimed to determine the effect of phytosterols and inulin on plasma glucose, insulin, and GLP-1 levels among healthy men after consuming phytosterols and inulin-enriched soymilk for 8 weeks.ResultsA total of 26 men at least 20 years old were randomly assigned into the 2 g/day of phytosterols and 10 g/day of inulin-enriched soymilk (intervention) group or into the standard soymilk (control) group. In the intervention group, the area under the curve of Glucagon-like peptide-1 secretion increased significantly, compared to its baseline (p = 0.003). The area under the curve of insulin secretion also increased but it did not meet statistical significance (p = 0.118). The area under the curves of plasma glucose were similar between pre- and post-test (p = 0.348). In the control group, none of the primary results significantly changed compared to their baseline levels.Trial registration Thai Clinical Trial Registry: TCTR20160319001 date: March 19, 2016, retrospectively registered.Electronic supplementary materialThe online version of this article (10.1186/s13104-018-3958-5) contains supplementary material, which is available to authorized users.