Despite decades-long research efforts, the remediation of groundwater contaminated by heavy metals has remained a significant challenge. Recent studies have demonstrated that in situ formation of magnetite might be an effective method to more permanently immobilize metal(loid)s. However, how the co-existence of additional heavy metals affects the synthesis of magnetite under environmentally relevant conditions and how it affects the associated heavy metal removal efficiency have remained unclear. Here, a common magnetite synthesis procedure was used to synthesize Cu-, Cd-, and Pb-substituted magnetites at circumneutral pH with variable heavy metal concentrations. The synthesized mineral products were then subjected to digestion, Mössbauer, XRD, SEM-EDS, magnetic susceptibility and surface area measurements, as well as isothermal adsorption experiments. The presence of additional divalent heavy metals during synthesis affected the characteristics of the Fe mineral products. Magnetite formed in the presence of heavy metals was poorly crystalline and impure. The mineralogy and morphology of the products was regulated by the surface affinity of the heavy metal. The co-existence of divalent heavy metal cations that have higher surface affinity than Fe(II) suppressed the mineral growth of more crystalline Fe oxides, including magnetite. Minerals synthesized in the absence of heavy metals had higher capacity and affinity for heavy metals than minerals synthesized in the presence of those metals because of the effects of altered mineral surface structure and surface area on adsorption. These results help us understand how different types and concentrations of heavy metals affect magnetite synthesis and its suitability for in situ groundwater remediation.