A large number of organic matter degradation, CO2 transport and dissolved organic matter models have been developed during the last decades. However, organic matter degradation models are in many cases hard-coded in terms of pools, kinetics and dependency on environmental variables. The input of the model user is typically limited to the adjustment of input parameters. In addition, the coupling with geochemical soil processes including aqueous speciation, sorption and colloid-facilitated transport are not incorporated in many of these models. Furthermore, these models are combined with simplified representations of flow and transport processes. We illustrate the capability of generic reactive transport codes to overcome these shortcomings. The formulations of reactive transport codes include a physics-based continuum representation of flow and transport processes, while biogeochemical reactions can be described as equilibrium processes and/or kinetic reaction networks. The flexibility of these type of codes allows for straightforward extension of reaction networks with new model components and in such a way facilitates an application-tailored implementation of organic matter degradation models and related processes. A numerical benchmark involving two reactive transport codes (HPx and MIN3P) demonstrates how the process-based simulation of transient variably saturated water flow, solute transport, heat transfer and diffusion in the gas phase can be combined with a flexible implementation of a soil organic matter degradation model. The benchmark includes the production of leachable organic matter and inorganic carbon in the aqueous and gaseous phases, as well as different decomposition functions with first-order, linear dependence or nonlinear dependence on a biomass pool. In addition, we show how processes such as local bioturbation (biodiffusion) can be included implicitly through a Fickian formulation of transport of soil organic matter. Coupling soil organic matter models with generic and flexible reactive transport codes offers a valuable tool to enhance insights into coupled physico-chemical processes at different scales within the scope of C-biogeochemical cycles, possibly linked with other chemical elements such as plant nutrients and pollutants.