The pursuit of developing healthier pasta products without compromising technological properties involves a strategic approach via the customization of raw material formulations and the integration of grain germination and extrusion processes. This study explores the impact of incorporating sprouts from quinoa (Chenopodium quinoa Willd) and kiwicha (Chenopodium pallidicaule Aellen) on the physicochemical properties of pasta by employing a centroid mixture design. The desirability function was utilized to identify the optimal ingredient proportions necessary to achieve specific objectives. The study identified optimal formulations for two pasta variations: pasta with the substitution of sprouted quinoa and cushuro powder (PQC), and pasta with partial substitution of sprouted kiwicha and cushuro powder (PKC). The optimal formulation for PKC was determined as 70% wheat flour (WF), 15% sprouted kiwicha flour (SKF), and 15% cushuro powder (CuP), with a desirability score of 0.68. Similarly, for PQC, the optimal formulation comprised 79% WF, 13% sprouted quinoa flour (SQF), and 8% CuP, with a desirability of 0.63. The optimized pasta formulation exhibited longer cooking times (10 and 8 min), increased weight gain (235% and 244%), and minimal loss of solids (1.4 and 1.2%) for PQC and PKC, respectively. Notably, firmness (2.8 and 2.6 N) and breaking strength values (2 and 2.7 N) for PQC and PKC pasta formulations, respectively, were comparable to those of the control sample (2.7 N and 2.6 N for firmness and fracturability, respectively). This research underscores the potential of tailored formulations and innovative processes to enhance the nutritional profile of pasta while maintaining key technological attributes.