Kañiwa (Chenopodium pallidicaule Aellen) is an Andean pseudocereal rich in protein and phenolic compounds, whose bioactive potential under controlled germination remains unexplored through simultaneous metabolite optimization. Germination conditions of kañiwa cv. Cupi were optimized using a Central Composite Design (CCD) and the Derringer–Suich desirability function, with time (24–96 h) and temperature (18–30 °C) as independent variables, and γ-aminobutyric acid (GABA), total soluble phenolic compounds (TSPC), ORAC, FRAP, and protein content as responses. Five second-order polynomial models yielded adjusted R² values of 0.703–0.880 with non-significant lack of fit (p > 0.050). Germination time was the dominant factor for GABA, TSPC, ORAC, and FRAP, while temperature exerted the predominant negative quadratic effect on protein content. Optimal conditions (96 h, 24 °C; D = 0.845) produced experimental increases of 1710.30% in GABA (26.12 mg GABA·100 g⁻¹), 117.10% in TSPC (926.9 mg GAE·100 g⁻¹), 261.40% in ORAC (51,756.0 µmol TE·100 g⁻¹), 244.10% in FRAP (1971.2 µmol TE·100 g⁻¹), and 42.34% in protein (16.05%) relative to ungerminated seeds. The GABA value constitutes the first report of this non-protein amino acid in germinated kañiwa under optimized conditions. Complementary analyses demonstrated that optimized germination markedly increased total reducing sugars and free glucose while decreasing amylolytic and glucoamylase activities and increasing lipase activity, confirming the extensive mobilization of carbohydrate reserves and the metabolic reprogramming associated with the germination process. These findings position kañiwa as a high-value functional ingredient for the Andean food industry.