Within soils, biogeochemical processes controlling elemental cycling are heterogeneously distributed owing, in large part, to the physical complexity of the media. Here we quantify how diffusive mass-transfer limitation at the soil aggregate scale controls the biogeochemical processes governing ferrihydrite reductive dissolution and secondary iron mineral formation. Artificial cm-scale aggregates made of ferrihydrite-coated sand inoculated with iron-reducing bacteria were placed in flow-through reactors, mimicking macro- and microporous soil environments. A reactive transport model was developed to delineate diffusively and advectively controlled regions, identify reaction zones and estimate kinetic parameters. Simulated iron (Fe) breakthrough-curves show good agreement with experimental results for a wide-range of flow rates and input lactate concentrations, with only a limited amount (< or =12%) of Fe lost in the reactor outflow over a 31 day period. Model simulations show substantial intra-aggregate, mm-scale radial variations in the secondary iron phase distributions, reproducing the trends observed experimentally where only limited transformation of ferrihydrite was found near the aggregate surface, whereas extensive formation of goethite/lepidocrocite and minor amounts of magnetite and/or siderite were observed toward the aggregate center. Our study highlights the important control of variations in transport intensities on microbially induced iron transformation at the soil aggregate scale.