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Innovation of pastry products towards higher nutritional and commercial value remains a challenge to the growing field of healthy food. In this study, the prebiotic supplementation and sugar reduction were explored in a widely consumed pastry product with a low level of innovation. The prebiotic potential of commercial agave inulin and galacto-oligosaccharides (GOS) was evaluated and compared by an in vitro model using human fecal inocula. Rice muffins containing 100% of sugar or 75% of sugar supplemented with 0.8% GOS were produced and compared with commercial rice muffins regarding their physical and textural properties. GOS fermentation led to the highest production of lactate and short-chain fatty acids, besides the most significant reduction of the final pH value and of the ammonia and methane production. Inulin presented a higher selectivity towards Lactobacillaceae (51 ± 1% of all), while GOS are more efficient to stimulate Bifidobacteriaceae growth (65 ± 7% of all). Both prebiotics were effective in reducing Methanobacteria. The reduction of sugar content modified the air bubbles characteristics (size and population with a greater number of tunnels) present in the muffin crumb, without relevant differences in apparent porosity. Textural results indicated that springiness and resilience of the muffin with low sugar content are acceptable, but hardness and chewiness were increased. The new-formula muffins presented very relevant textural parameters with comparable values to those reported in the literature for the commercial ones, thus anticipating a good consumer acceptance. This study is an important contribution towards more innovative and diversified healthy pastry products. [Display omitted] • The in vitro fermentation of inulin and GOS was evaluated using human fecal inocula. • GOS led to the highest bifidogenic effect and production of SCFA and gases. • Both prebiotics were effective in reducing Methanobacteria and Proteobacteria. • Rice muffins formulated with GOS and sugar reduction were produced. • Sugar reduction did not alter significantly springiness and resilience of the cakes. [ABSTRACT FROM AUTHOR]