Abstract Numerical simulations concerning iron–clay interactions in the conditions of an integrated experiment were conducted within a Callovo-Oxfordian claystone block at 90°C for 2 years. The calculations aim at determining the configurations and the parameters for which the simulation reproduce the mineral paragenesis observed at the end of the experiment. This paragenesis suggests that a thin magnetite layer precipitates at the surface of the corroding iron and dissolves on the claystone side to promote precipitation of Fe-silicate and Fe-carbonate minerals. The claystone is also altered close to the interface with iron via a significant precipitation of a Fe-carbonate mineral. The results obtained using the coupled reactive transport code Crunchflow show that adjusting both the kinetics of magnetite dissolution/precipitation and the properties of the corroded layer (considered as a diffusive barrier) was required in order: (i) to model the destabilization of the magnetite layer formed at the original iron–claystone interface early in the corrosion process and the precipitation of other iron-bearing minerals; and (ii) to isolate the chemical conditions at the iron surface from the conditions in the clay environment in order to favour magnetite precipitation at the iron surface. With these assumptions, the model closely reproduced the mineral paragenesis observed in the experiment.