Gluten Free (GF) diet is poor in fibre mainly due to the low intake of whole grains and the low fibre content of GF products that are usually based on starches and/or refined flours. The incorporation of alternative flours rich in fibre in the formulation of baked goods could improve their technological quality and consumer’s health. In this sense, the addition of novel flours from the grinding of endocarp-seed (ES) and exocarp-mesocarp (EM) of Neltuma affinis fruit, in the design and formulation of GF bread was studied. The aim of this study was to evaluate the effects of different levels of ES, EM and water hydration (WH) on the alveolar structure, pH and colour of GF bread. A Box–Behnken experimental design (three factors: ES; EM; WH and three levels: -1; 0; +1), was applied. The results showed that EM and ES had a negative effect on the pH. The alveolar structure of crumb was significantly affected by WH, showing a greater alveolar size with the higher levels of WH, and a greater cell density and homogeneity with the lower levels. The three factors studied presented a significant and positive effect on coordinate a*; however, the interaction ES-EM had an antagonistic effect on this parameter. It can be concluded that the three factors studied showed an effect on technological parameters of GF bread. The inclusion of flours N. affinis flours could be a useful tool to improve the nutritional profile of LG bread and give added value to this species.