Germination is an effective strategy to improve the nutritional and functional quality of Andean grains such as quinoa (Chenopodium quinoa Willd.); it helps reduce anti-nutritional components and enhance the digestibility and sensory aspects of the germinated. This work aimed to evaluate the effect of germination (0, 24, 48, and 72 h) on the physicochemical properties, content of bioactive compounds, and antioxidant capacity of three varieties of quinoa: white, red, and black high Andean from Peru. Color, nutritional composition, mineral content, phenolic compounds, flavonoids, and antioxidant activity were analyzed. Additionally, infrared spectra were obtained to elucidate structural changes during germination. The results showed color variations and significant increases (p < 0.05) in proteins, fiber, minerals, phenolic compounds, flavonoids, and antioxidant capacity after 72 h of germination, attributed to the activation of enzymatic pathways. In contrast, the infrared spectra showed a decrease in the intensity of functional groups –CH–, –CH₂–, C–OH, –OH, and C–N. Correlation analysis showed that flavonoids mainly contributed to antioxidant activity (r = 0.612). Germination represents a promising alternative to develop functional ingredients from germinated quinoa flour with improved nutritional and functional attributes.