The purpose of this study was to compare the effects of quinoa versus multigrain supplementation on glycemia and lipid metabolism among individuals with impaired glucose tolerance (IGT). In total, 207 participants diagnosed with IGT were randomly assigned to the quinoa group (QG; 100 g day-1, replacing about half of the total daily staple food), multiple whole grain group (WGG; 100 g day-1), or control group (CG) and followed for one year. Biomarkers were measured before and after the intervention. At the efficacy endpoint, the quinoa group (QG) demonstrated significantly longer time in range (TIR) and normal glucose tolerance (NGT) conversion rate, along with lower rates of 2-hour postprandial glucose (2hPG), fasting insulin (FINS), homeostatic model assessment of insulin resistance (HOMA-IR), 14-day mean blood glucose (14dMBG), and diabetes mellitus development compared to those of the multigrain and control groups (P < 0.05). Significant improvements in glycated hemoglobin (HbA1c) were also found in both the quinoa and multigrain groups compared to the control group (P < 0.05). No significant difference in glycemic variability (CV) was observed between the quinoa and control groups, while a significant difference was observed between the quinoa and multigrain groups (P < 0.05). These results suggest that quinoa consumption is significantly more effective than a multiple whole-grain diet in controlling IGT by reducing postprandial glucose and HbA1c levels, improving insulin resistance, and enhancing lipid profiles, making it a superior dietary choice for managing IGT.