Developing gluten-free (GF) pasta with high nutritional and technological quality remains a critical challenge for the food industry, requiring the substitution of gluten with alternative matrices. This study evaluated the effect of incorporating exocarp-mesocarp flour obtained from the milling process of Neltuma affinis pod (EMF: 0–10 g/100g), soybean extruded–expelled meal (SEE: 0–10 g/100g), and dough hydration level (WH: 35.5–40.5 mL/100g) on the technological properties of GF fresh pasta. A Box-Behnken design with three central points by triplicate was implemented. Optimal cooking time (OCT) and mass gain (MG) were determined using standard AACC methods. Colour profiles (L*, a*, b*, Chroma, and ΔE; CIELAB) were evaluated in cooked pasta. Model adequacy was corroborated by coefficient of determination (R2) > 70%, Durbin-Watson statistics > 1, and lack-of-fit tests ≥ 0.05. All response variables were fitted to a second-order polynomial model. OCT was significantly affected (p<0.05) by a negative linear effect and a positive quadratic effect of SEE, describing a parabolic behaviour. MG exhibited a pronounced curvature with positive quadratic effects for all factors studied and a significant synergetic EMF-SEE interaction (p<0.05); where the combined incorporation of maximum levels of EMF and SEE promoted a dense matrix increasing MG. As regard chromatic profiles (p<0.05), EMF reduced L* and increased a*, whereas SEE enhanced b* via linear and positive quadratic effects. Chroma exhibited a negative linear and a positive quadratic EMF effect, denoting lower purity at intermediate levels and specific pigment dilution. ΔE analysis revealed that EMF increased thermal sensitivity, whilst both higher WH levels and SEE exerted a protective, stabilising effect on surface colour. The strategic combination of local regional flours and soy by-products, as functional ingredients, allows for the improvement of the technological properties of GF fresh pasta.