A novel, modified polypyrrole/m-phenylediamine (PPy–mPD) composite, decorated with magnetite (Fe3O4) nanoparticles, and prepared via an in-situ oxidative polymerisation, was investigated. The PPy–mPD/Fe3O4 nanocomposite was employed for the removal of highly toxic oxyanion hexavalent chromium Cr(VI) from an aqueous solution. The structure and successful formation of the PPy–mPD/Fe3O4 nanocomposite was confirmed and investigated using various techniques. The presence of Fe3O4 was confirmed by high resolution transmission electron microscopy, with an appearance of Fe lattice fringes. The estimation of the saturation magnetisation of the nanocomposite, using a vibrating sample magnetometer, was observed to be 6.6 emu/g. In batch adsorption experiments, PPy–mPD/Fe3O4 nanocomposite (25 mg) was able to remove 99.6% of 100 mg/L of Cr(VI) at pH 2 and 25 °C. Adsorption isotherms were investigated at different Cr(VI) concentration (100–600 mg/L) and temperature (15–45 °C). It was deduced that adsorption follows the Langmuir model, with a maximum adsorption capacity of 555.6 mg/g for Cr(VI) removal. Furthermore, isotherm data were used to calculate thermodynamic values for Gibbs free energy, enthalpy change and entropy change, which indicated that Cr(VI) adsorption was spontaneous and endothermic in nature. Adsorption–desorption experiments revealed that the nanocomposite was usable for two consecutive cycles with no significant loss of adsorption capacity. This research demonstrates the application potential for the fascinating properties of PPy–mPD/Fe3O4 nanocomposite as a highly efficient adsorbent for the removal of heavy metal ions from industrial wastewater.