Wheat flour replacement by rice flour is a key strategy in gluten-free batter production. Rice flour needs hydrocolloids to offset the development of the network of the mix. In this context, the aim of this work was to analyze the influence of chitosan (0–1 g/100 g of batter) addition on the microstructural, rheological and thermal properties of wheat:rice flours batters (100:0; 70:30, 30:70 and 0:100 (g/g)). Results showed that increasing replacement of wheat flour by rice one decreased the consistency (K) and the yield stress (τ0), and increased the flow behavior index (n) because of the absence or lower gluten content. However, the addition of only 0.25 g/100 g chitosan to rice flour formulation (0:100 (g/g)) increased its viscosity (from 371 to 1006 mPa s), exhibiting a rheological behavior similar to wheat flour formulation (100:0 (g/g) (1050 mPa s)). Chitosan enhanced consistency and structural agglomeration, and the interaction among ingredients, especially in batters with high content of rice flour (30:70 and 0:100 (g/g)). Lastly, chitosan incorporation did not significantly modify thermal properties, excepting in rice-flour batters (0:100 (g/g)), reducing Tm, ΔHm, and thus, increasing the bound water content (from 17 to 32 g/100 g). •Chitosan (CH) increases viscosity in rice flour-based batters.•CH addition to rice flour based-batters improves structural agglomeration.•CH addition to wheat-rice flours batters do not influence their thermal behavior.