Fe minerals sorb nutrients and pollutants and participate in microbial and abiotic redox reactions. Formation and transformation of Fe minerals is typically followed by mineral analysis at different time points. However, in lab studies the available sample amount is often limited and sampling may even influence the experimental conditions. We therefore evaluated the suitability of in situ magnetic susceptibility (MS) measurements, which do not require sampling, as an alternative tool to follow ferro(i)magnetic mineral (trans-)formation during ferrihydrite reduction by Shewanella oneidensis MR-1, and in soil microcosms. In our experiments with MR-1, a large initial increase in volume specific MS (kappa) followed by a slight decrease correlated well with the initial formation of magnetite and further reduction of magnetite to siderite as also identified by micro-XRD. The presence of humic acids retarded magnetite formation, and even inhibited magnetite formation completely, depending on their concentration. In soil microcosms, an increase in kappa accompanied by increasing concentrations of HCl-extractable Fe occurred only in microbially active set-ups, indicating a microbially induced change in soil Fe mineralogy. Based on our results, we conclude that MS measurements are suitable to follow microbial Fe mineral transformation in pure cultures as well as in complex soil samples.