Consumer acceptance testing found wheat flour alternatives can be combined with rare sugars to create acceptable lower sugar, gluten-free muffins. Muffins were developed and optimized using an initial screening procedure. A simplex centroid mixture design defined combinations of wheat-flour alternates. Ninety-one randomized baked blends were analyzed and compared for physical and basic sensory attributes using numerical optimization techniques. Blends of almond flour, whey protein concentrate, and a 50/50 blend of oat fibre and resistant maltodextrin achieved desired structures for high-protein and high-fibre muffins. Combinations of non-dairy coconut creamer, whey protein concentrate, and the same blend of oat fibre and maltodextrin composed the high-fat variant. Optimized flour replacement blends enabled a sugar replacement comparison in a separate categorical design. Vanilla-flavored muffins formulated with monosaccharides (allulose or tagatose) or sucrose (as a control), had sweetness levels augmented with stevia to theoretically equivalent levels. Muffins with allulose or tagatose differed from those containing sucrose in water activity and crust colour (lightness, L*). Overall liking for sucrose substituted formulations compared favorably in a consumer acceptance panel (n = 58). After providing the nutritional composition for sampled products at the conclusion of the sensory analysis, purchase intent of sugar substituted products was comparable to the control muffins.