Background and aim <p>The remediation effects and underlying mechanisms of intercropping on iron and manganese contamination in coal gangue dumps remain to be further elucidated.</p> Methods <p>This study employed a leaching column experiment to evaluate the effects of intercropping <i>Pennisetum giganteum</i> Z.X.Lin and <i>Medicago sativa</i> L. on Fe/Mn concentrations, chemical fraction in coal gangue-contaminated soil and plant root responses.</p> Results <p>Results demonstrated that: (1) The intercropping synergistically regulated Fe/Mn distribution and fraction in coal gangue soils, reducing the concentration of Fe and Mn in deep soil layer (20-40 cm) by 4.55%-5.04%, 12.01%-14.10%, respectively, as compared to control group. Residual Fe and acid-extractable Mn proportions increased by 8% and 7%, respectively. (2) Intercropping significantly increased specific root length and root tissue density, with specific root surface area identified as a key influencing factor for Fe/Mn content in the coal gangue soil. Intercropping significantly enhanced the Fe content in roots of <i>M. sativa</i> by 78.96% and Mn content in shoot by 23.51%. Similarly, it significantly increased the Fe and Mn content in the roots of <i>P. giganteum</i> by 21.99% and 23.81%, respectively, and promoted the transformation of Fe and Mn within the plants into residual fractions. (3) The intercropping system reduced Fe/Mn leaching outputs by 34.80% and 11.75%, respectively. Cropping pattern and root iron plaque Mn content were identified as primary drivers for Fe/Mn leaching, respectively.</p> Conclusions <p><i>P. giganteum</i>/<i>M. sativa</i> intercropping reduces Fe/Mn diffusion via complementary root vertical zonation, providing an effective technical approach for ecological restoration of coal gangue dumps.</p>