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Mine wastewater (MW) is often rich in heavy metals that can have measurable effects on humans. The storage and treatment of MW remains a challenge for most mining companies. Iron (Fe) in MW was removed by using extracts from Eucalyptus globulus (EG); Callistemon viminalis (CV); and Persea americana (AS). Fe was removed from MW samples with an initial concentration of 5.53 mg Fe mL−1; 4.63 mg Fe mL−1 and 4.40 mg Fe mL−1 using EG leaves, CV flowers and AS seed extracts, respectively. Conditions of the MW decontamination were studied by varying the dosage of the plant extracts, the temperature of the medium and the contact time between the MW and the plant extracts. Undiluted plant extracts—which were mixed with the MW and heated at 45 °C for 3 h—gave the highest Fe-removal efficiency for CV (70%) and AS (53%) extracts, respectively. Similarly, EG extracts, albeit heated at 25 °C, showed a higher Fe-removal efficiency (85%) than the CV and AS extracts at low to high temperatures. The residual Fe concentration in the MW was 0.83 mg Fe mL−1, 1.39 mg Fe mL−1 and 2.07 mg Fe mL−1 for EG, CV and AS extracts, respectively. Residue solid-phase deposits from the precipitation reaction of the MW with the plant extracts were collected and analyzed. Fe was among the byproducts detected in the deposited material. The characterization of the annealed solid-phase deposits revealed Fe precipitates as maghemite-C (Fe2O3) and magnetite (FeFe2O4) nanoparticles. Therefore, the MW quality and form were improved, making it reusable for other purposes