Abstract. Microbial communities, comprising phototrophic and heterotrophic microorganisms, play a crucial role in global biogeochemical cycles. However, existing biogeochemical models rarely take into account the complex interactions between these groups, usually focusing on competition for resources. In this work, we introduce the Microbial Community Model (MCoM), a framework for simulating the dynamics of diverse microbial communities. MCoM incorporates a wide range of interactions, such as cross-feeding, metabolite effects, and competition for nutrients. The model differentiates between dissolved organic nutrients (DON) and carbon (DOC), accounts for phytoplankton and heterotrophic bacterial species-specific organic matter release and uptake profiles, and simulates the impacts of bacterial metabolites on phytoplankton growth. Implemented as a box model, MCoM tracks phototrophic and heterotrophic biomass, active metabolites, DOC, DON, and inorganic nutrients through non-linear differential equations, enabling the exploration of emergent properties and feedbacks. We demonstrate the model's capabilities through simulations of experimental data of pairwise co-cultures of heterotrophic and phototrophic microorganisms, and find overall good agreement. Due to the scalable implementation, interaction matrices for larger, i.e. hundreds, of microbial groups can easily be realised. We show examples for such applications of MCoM in assessing emergent dynamics, including periodic succession patterns and multi-stability. MCoM provides a versatile, scalable, and customizable platform for assessing the range from pairwise interactions to complex microbial communities and their impact on biogeochemical fluxes.