Increased demand for quinoa as a functional food has resulted in more quinoa-growing areas and initiatives to increase grain production, particularly in organic agriculture. Quinoa seeds are a superfood with incredible nutritional benefits. They are abundant in secondary metabolites with significant medicinal activity. This report was consequently performed to investigate whether Azolla fliculoides (AE) or moringa leaf extract (MLE) foliar spray can be supplemented as organic extracts to enhance quinoa growth and productivity under organic farming. Three quinoa cultivars, KVL–SRA2 (C1), Chipaya (C2), and Q–37 (C3), were grown organically and subjected to foliar spraying with AE or MLE at a 20% ratio, as well as their combination (AE+MLE). Plant performance of the three cultivars was significantly enhanced by MLE or AE applications as compared with control plants. The highest outputs were obtained by AE+MLE treatment, which significantly increased the seed yield by about 29% as compared with untreated plants. Seed quality exhibited a marked increase in response to AE+MLE that was superior in this regard as it showed higher protein, carbohydrates, saponine, tannins, phenolics, and flavonoids content. The C3-cultivar demonstrated the highest productivity, saponine, and flavonoids levels as compared to the other cultivars. Overall, the current study indicated that foliar spray with AE+MLE could enhance growth and productivity as well as quality and pharmaceutical active ingredients of quinoa cultivars grown under farming conditions.