This article analyses, the replacement of sucrose in muffins with nine different combinations of isomaltulose and oligofructose. Being a structural isomer of sucrose with approx. 50% of sucrose sweetness, isomaltulose is non‐cariogenic and with a low glycemic profile but having the same calories as sucrose. Oligofructose is composed of fructose polymers, with a reduced caloric value and prebiotic effect. Specifically, height, percentage of alveoli, water content, Aw, mechanical, and optical properties have been measured along with a sensory evaluation. The results showed that all combinations of sweeteners gave place to softer muffins than control ones. Moreover, isomaltulose caused a darkening of the products likely due to an enhancement of the Maillard reactions. The highest amount of isomaltulose and the absence of sucrose meant the worst score in sweetness and flavor due to the low sweetening powder of isomaltulose.