Heavy metal pollutants in the environment are of global concern due to their risk of contaminating drinking water and food supplies. Removal of these metals can be achieved by adsorption to mixed-valent magnetite nanoparticles (MNPs) due to their high surface area, reactivity, and ability for magnetic recovery. The adsorption capacity and overall efficiency of MNPs are influenced by redox state as well as surface charge, the latter of which is directly related to solution pH. However, the influence of microbial redox cycling of iron (Fe) in magnetite alongside the change of pH on the metal adsorption process by MNPs remains an open question. Here we investigated adsorption of Cd and Cu by MNPs at different pH values that were modified by microbial Fe(II) oxidation or Fe(III) reduction. We found that the maximum adsorption capacity increased with pH for Cd from 256 μmol/g Fe at pH 5.0 to 478 μmol/g Fe at pH 7.3 and for Cu from 229 μmol/g Fe at pH 5.0 to 274 μmol/g Fe at pH 5.5. Microbially reduced MNPs exhibited the greatest adsorption for both Cu and Cd (632 μmol/g Fe at pH 7.3 for Cd and 530 μmol/g Fe at pH 5.5 for Cu). Magnetite oxidation also enhanced adsorption of Cu but inhibited Cd. Our results show that microbial modification of MNPs has an important impact on the (im-)mobilization of aqueous contaminations like Cu and Cd and that a change in stoichiometry of the MNPs can have a greater influence than a change of pH.