<p>Quinoa (<i>Chenopodium quinoa</i>) is increasingly integrated into diets due to its high nutritional value, antioxidant activity and health benefits. This study aimed to systematically evaluate the influence of varying germination times (0, 12, 18, 24, and 36&#xa0;h) on quinoa’s nutritional, physicochemical, functional, antioxidant, anti-nutritional, pasting, thermal, and structural properties. A combination of analytical techniques, including proximate analysis, FTIR, and pasting profile analysis, was employed to investigate these effects. Germination resulted in a significant (<i>p</i> &lt; 0.05) increase in protein and fibre content, while a reduction in ash, fat, and carbohydrates was observed, likely due to enzymatic activity promoting macronutrient mobilization during different germination stages. Functional properties of the flour were altered, with significant (<i>p</i> &lt; 0.05) increases in antioxidant activity (31.32% in total phenolic content, 40.21% in total flavonoid content), attributed to the release of bound phenolic compounds. Antinutritional factors, including saponin and phytic acid, were significantly (<i>p</i> &lt; 0.05) reduced (30.11% and 42.46%), possibly due to enzymatic degradation and leaching. Germination significantly (<i>p</i> &lt; 0.05) decreased setback, breakdown, final viscosity, and pasting temperature, indicating starch breakdown. FTIR analysis revealed shifts in functional groups, reflecting structural changes in the flour, while alterations in morphology and thermal properties were also noted. The findings from this study highlight the role of germination time in modifying quinoa’s nutritional and functional properties for diverse food applications.</p>