Background and Objectives Iron‐deficiency anemia (IDA) is the most common form of nutritional anemia in both developed and developing countries. We aimed to evaluate the germination impact on the nutritional profile of quinoa seeds and the antianemic potentials of quinoa fortified phytogenic diet in treatment of iron‐deficiency anemia‐induced albino rats. Findings The results revealed that quinoa seeds are considered a good source of fiber, protein (43.08 and 30.62% of DV), and vitamin C (threefold of daily requirement). Germination of the seeds increased iron, calcium, and zinc contents by 39.43, 49.04, and 20.25%, vitamin C and carotenoids by 32.17 and 26.02%, respectively, and decreased antinutritional factors saponin, phytic acid, and tannins by 59.60, 50.0, and 11.32%, respectively. The biological assay indicated that fortification with 10% quinoa sprouts (GII6) can be recommended as the best treatment to restore body weight, organs weights, serum profile (protein, ferritin, iron, and zinc), and blood cell counts (RBCs, WBCs, Hb, and platelets), as reflected in red cell indices (Hct, MCV, MCH, and MCHC) of IDA induced rats being at optimum levels, which were comparable to the healthy rats group (GI). Conclusion Increased antioxidants, vitamins, minerals content, and bioavailability of nutritional compounds due to decreased antinutritional factors content in the germinated sprouts resulted in antianemic health potentials in treated rats. Significance and Novelty Evidence indicates that germinated quinoa seeds are superior in nutrients compared to the ungerminated seeds due to the activation of endogenous enzymes that degrade antinutritional factors, elevate mineral bioavailability and antioxidant properties. Trial registration number: AU08190625330; Date of registration: 25–06–2019.