This study describes the coupling of the process-based Model of Early Diagenesis in the Upper Sediment with Adaptable complexity (MEDUSA version 2) to an existing ocean biogeochemistry model consisting of the Finite-volumE Sea ice–Ocean Model (FESOM version 2.1) and the Regulated Ecosystem Model (REcoM version 3). Atmospheric CO2 in the model is a prognostic variable which is determined by the carbonate chemistry in the surface ocean. The model setup and its application to a pre-industrial control climate state is described in detail. In the coupled model, 1390 PgC is stored in the top 10 cm of the bioturbated sediment, mainly as calcite, but also as organic matter (10 %). In the coupled simulation, atmospheric CO2 stabilizes at ∼295 ppm after 2000 years, in line with the CO2 level expected from the climate forcing conditions. Sediment burial of carbon, alkalinity, and nutrients in the coupled simulation is set to be compensated by riverine input. The spatial distribution of biological production is altered depending on the location of riverine input and reduction in sedimentary input, as well as the strength of local nutrient limitation, while the global productivity is not affected substantially. With this coupled ocean–sediment system the model is able to simulate the carbonate compensation feedback under moderate perturbation of CO2 in the atmosphere.