BACKGROUND Cowpea (Vigna unguiculata L. Walph) is predominantly consumed in the North and Northeast regions of Brazil, and its biofortification with iron seeks to reduce the high prevalence of iron deficiency anemia in these regions. It is commonly eaten cooked; however, in the germinated form, it can improve nutritional quality by reducing the antinutritional factors and consequently improving the bioavailability of elements. The present study aimed to determine the physico‐chemical characteristics, bioaccessibility and bioavailability of iron in biofortified germinated cowpea. RESULTS There was no statistical difference between the germinated and cooked beans with regard to centesimal composition. Germinated beans had phytates and tannins similar to cooked beans. The phytate‐iron molar ratio for all groups did not present a statistical difference (cooking 3.58 and 3.41; germinated 3.94 and 3.51), nor did the parameters evaluating in vivo iron bioavailability. Total phenolics was higher in the germinated group (cooking 0.56 and 0.64; Germinated 2.05 and 2.45 mg gallic acid kg−1). In vitro bioaccessibility of iron of germinated beans presented higher values (P ≤ 0.05) compared to cooked beans. There was higher expression of divalent metal transporter‐1 in biofortified and germinated beans. CONCLUSION The iron bioavailability from the biofortified and germinated beans was comparable to ferrous sulfate. Germination can be considered as an alternative and efficient method for consuming cowpea, presenting good iron bioaccessibility and bioavailability. © 2019 Society of Chemical Industry