ALT Biogeochemical models inadequately capture microscale soil carbon effects, leading to conflicting portrayals of soils as carbon sinks or sources at the ecosystem level under climate change. New models, though promising, face significant challenges due to their growing complexity and scarcity of data for validation. A key difficulty lies in determining how to effectively incorporate the variability of microscale ecosystem processes, which reflect variations of microbiome diversity, and encompass the physiological, hydrological, as well as mineralogical characteristics of soil microhabitats shaped by past selection. This special feature will present interdisciplinary insights into soil carbon dynamics, examining how microscale interactions and microbial diversity affect carbon and nutrient cycles at the ecosystem scale.