Environmental context.Microbial ecosystems are characterised by the interplay of various microorganisms with their biotic and abiotic environment. Biogeochemical niches host adapted microbial communities that are in constant competition for substrates and nutrients. Their natural distribution, interactions and responses to fluctuating environmental conditions are often impossible to simulate in laboratory studies. Using biogeochemical iron redox cycling as an example, we suggest the application of a conceptual framework to improve our understanding of the principal functioning of (geo)microbial ecosystems. Abstract.Our knowledge on how microbial ecosystems function profits from the support of biogeochemical concepts which describe the cycling of elements through various geochemical gradients. Using the example of the iron cycle in freshwater sediments, we propose a theoretical framework that describes the dynamic interactions between chemical and microbial FeII oxidation and FeIII reduction, their spatial location and how they are affected by changing environmental conditions. This contribution emphasises the complexity ecological research faces when dealing with heterogeneous and dynamic natural systems. Our concept aims to provide further insights into how flows of energy and matter are controlled during microbial and chemical Fe redox transformations and how various key variables, such as substrate availability and competition as well as thermodynamic and kinetic parameters, affect flow directions.