We hypothesized that optimizing the formulation of pasta by incorporating sprouted pseudocereal flours, specifically quinoa (Chenopodium quinoa Willd) or kiwicha (Amaranthus caudatus L.) and cushuro (Nostoc sphaericum Vaucher ex Bornet & Flahault) flours, could offer the potential to simultaneously enhance nutritional quality and health-promoting properties in pasta. In this study, our objective was to optimize the formulation of composite flour (a ternary blend of wheat, sprouted pseudocereal, and cushuro flours) using a mixture composite design to maximize total soluble phenolic compounds (TSPC), γ-aminobutyric acid (GABA), antioxidant activity, and mineral bioaccesilability by reducing phytic acid (PA) content. Two optimal formulations were identified: one consisting of 79% wheat flour (WF), 13% SQF, and 8% CuF (oPQC), and the other composed of 70% WF, 15% SKF, and 15% CuF (oPKC). These optimized pastas exhibited reduced starch content and notably higher levels of total dietary fiber (1.5–3.61-fold), protein (1.16-fold), fat (1.3–1.5-fold), ash (2.2–2.7-fold), minerals (K, Na, Fe, Zn, Mg, Mn, and Ca), PA (3–4.5-fold), TSPC (1.3–1.9-fold), GABA (1.2–2.6-fold), and ORAC (6.5–8.7-fold) compared to control pasta (100% WF). Notably, the glycemic index of oPQC (59.8) was lower than that of oPKC (54.7) and control pasta (63.1). The nutritional profile of the optimized pasta was largely retained after cooking, although some significant losses were observed for soluble dietary fiber (18.2–44.0%), K (47.5–50.7%), Na (42.5–63.6), GABA (41.68–51.4%), TSPC (8–18%), and antioxidant activity (45.4–46.4%). In vitro digestion of cooked oPQC and oPKC demonstrated higher bioaccessible content of GABA (6.7–16.26 mg/100 g), TSPC (257.7–261.8 mg GAE/100 g), Ca (58.40–93.5 mg/100 g), and Fe (7.35–7.52 mg/100 g), as well as antioxidant activity (164.9–171.1 µmol TE/g) in intestinal digestates compared to control pasta. These findings suggest that the incorporation of sprouted pseudocereals and cushuro flour offers a promising approach to enhance the nutritional quality and bioactive content of wheat-based pasta, potentially providing health benefits beyond traditional formulations.