In soil, iron (Fe) solubility depends on complex interactions between Fe minerals and organic matter, but very little is known about plant availability of Fe present in Fe oxides associated with humic substances. For this purpose, this study investigates the effect of Fe mineral crystallinity in the presence of humic acids (HA) on Fe availability to plants. Four Fe–HA mineral coprecipitates were prepared, either in the presence or absence of oxygen, i.e., two goethite (G)‐HA samples containing large amounts of Fe as nanocrystalline goethite and ferrihydrite mixed phases, and two magnetite (M)‐HA samples containing crystalline magnetite. Bioavailability studies were conducted in hydroponic systems on cucumber plants (Cucumis sativus L.) grown under Fe deficient conditions and supplied with the Fe–HA coprecipitates containing goethite or magnetite. Results showed that plants grown in the presence of Fe–HA coprecipitates exhibited a complete recovery from Fe deficiency, albeit less efficiently than plants resupplied with Fe‐chelate fertilizer used as control (Fe‐diethylene triamine penta acetic acid, Fe‐DTPA). However, the supply with either G‐ or M–HA coprecipitates produced different effects on plants: G–HA‐treated plants showed a higher Fe content in leaves, while M–HA‐treated plants displayed a higher leaf biomass and SPAD (Soil–Plant Analysis Development) index recovery, as compared to Fe‐DTPA. The distribution of macronutrients in the leaves, as imaged by micro X‐ray fluorescence (µXRF) spectroscopy, was different in G–HA and M–HA‐treated plants. In particular, plants supplied with the poorly crystalline G–HA coprecipitate with a lower Fe/HA ratio showed features more similar to those of fully recovered plants (supplied with Fe‐DTPA). These results highlight the importance of mineral crystallinity of Fe–HA coprecipitates on Fe bioavailability and Fe uptake in hydroponic experiments. In addition, the present data demonstrate that cucumber plants can efficiently mobilize Fe, even from goethite and ferrihydrite mixed phases and magnetite, which are usually considered unavailable for plant nutrition.