In the presence of methanoate as electron donor, Shewanella putrefaciens, a Gram-negative, facultative anaerobe, is able to transform lepidocrocite (γ-FeOOH) to secondary Fe (II–III) minerals such as carbonated green rust (GR1) and magnetite. When bacterial cells were added to a γ-FeOOH suspension, aggregates were produced consisting of both bacteria and γ-FeOOH particles. Recently, we showed that the production of secondary minerals (GR1 vs. magnetite) was dependent on bacterial cell density and not only on iron reduction rates. Thus, γ-FeOOH and S. putrefaciens aggregation pattern was suggested as the main mechanism driving mineralization. In this study, lepidocrocite bioreduction experiments, in the presence of anthraquinone disulfonate, were conducted by varying the [cell]/[lepidocrocite] ratio in order to determine whether different types of aggregate are formed, which may facilitate precipitation of GR1 as opposed to magnetite. Confocal laser scanning microscopy was used to analyze the relative cell surface area and lepidocrocite concentration within the aggregates and captured images were characterized by statistical methods for spatial data (i.e. variograms). These results suggest that the [cell]/[lepidocrocite] ratio influenced both the aggregate structure and the nature of the secondary iron mineral formed. Subsequently, a [cell]/[lepidocrocite] ratio above 1 × 107 cells mmol−1 leads to densely packed aggregates and to the formation of GR1. Below this ratio, looser aggregates are formed and magnetite was systematically produced. The data presented in this study bring us closer to a more comprehensive understanding of the parameters governing the formation of minerals in dense bacterial suspensions and suggest that screening mineral–bacteria aggregate structure is critical to understanding (bio)mineralization pathways.