It is well-appreciated that the diet is a crucial tool to counteract cardiometabolic disturbances due to its impact on blood glucose concentration and gut microbiome. This retrospective analysis aimed to examine whether the inclusion of isomaltulose and prebiotic inulin-type fructans (ITF) into the habitual diet has an impact on glycemic control and gut microbiota. Furthermore, we examined interindividual differences in glycemic response to sugar replacement with isomaltulose. We retrospectively analyzed data of 117 individuals who participated in a digital nutrition program including a 14-day continuous glucose measurement. Participants underwent six test days with sweetened drinks (isomaltulose vs. sucrose) consumed with their usual breakfasts and lunches. Dinner was supplemented with ITF for 11 days. Postprandial glycemia and 24 h-glycemic variability were determined following test meals and days, respectively. Fecal microbiota was analyzed by 16S rRNA sequencing before and after test phase. Meals with isomaltulose-sweetened drinks compared to meals with sucrose-sweetened drinks induced lower postprandial glycemia. Moreover, glucose oscillations over 24 h were lower on isomaltulose when compared to sucrose test days and improved further during ITF supplementation. Furthermore, ITF modulated gut microbiota composition beneficially. Responder analysis revealed that 72% of participants benefited from the sugar replacement with isomaltulose and that their gut microbiota differed from the low responders. Taken together, the incorporation of isomaltulose and ITF into the habitual diet was shown to be an effective strategy to improve glucose control and beneficially modulate gut microbiota, and thereby aid to maintain metabolic health. Data indicate interindividual differences in glycemic response to ingredients and suggest that gut microbiota might be somehow related to it.