The high sucrose content in sweet bakery products is a nutritional concern. However, the technological functions of sucrose in such products make its replacement challenging. d-allulose, which only has 5% of the energy content of sucrose, may be an ideal sucrose substitute, due to its similar physicochemical and bulk properties. The aim of this study was to investigate the performance of d-allulose as the main sugar component in cupcakes, in comparison to both sucrose and d-fructose, by assessing the physicochemical and physical properties of cupcakes baked for 12, 16, and 20 min. d-allulose batters experienced less volume expansion and took longer to lose weight and thermally set during baking than did sucrose batters. d-allulose cupcakes had lower water activity values at all baking times and developed a browner colour and greater acrylamide concentration, compared to sucrose cupcakes. Comparable textural properties were achieved by d-allulose and sucrose cupcakes at the longest baking time (20 min). d-allulose and d-fructose produced cupcakes with comparable physical properties. There is potential for the use of d-allulose in the bakery products industry, by employing longer baking processes, or in other products requiring lower moisture content and less volume development.