Due to its impact on blood glucose and gut microbiota, diet is fundamental to counteract cardiometabolic disturbances. Evidence suggests higher effectiveness of personalized approaches compared to general recommendations explained by high interindividual variability. This retrospective analysis aimed to examine whether the inclusion of isomaltulose and prebiotic inulin-type fructans (ITF) into the habitual diet of persons living their usual lifestyle has an impact on glycemic control and gut microbiota. Furthermore, we examined interindividual differences in glycemic response to sugar replacement with isomaltulose. Therefore, 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 eleven days. Postprandial glycemia and 24h-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 hours were lower on isomaltulose when compared to sucrose test days and improved further in the course of ITF supplementation. In addition, ITF modulated gut microbiota composition beneficially (e.g., ↑Bifidobacteria). Responder analysis using 24h-glycemic variability revealed that 72% of participants particularly benefited from the sugar replacement with isomaltulose and that their gut microbiota differed from the low responders (e.g., ↑Eubacterium, ↓Parabacteroides). 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 indicates interindividual differences in glycemic response to ingredients and suggest that gut microbiota might be somehow related to it.