Nitrogen use in agriculture often prioritizes immediate yield gains at the expense of the environment and agroecosystem health. This problem persists because current solutions for crop nitrogen use inefficiency focus too narrowly on inputs and overlook the internal processes that govern nitrogen’s fate, from crop uptake and environmental losses to storage and transfers between various organic pools. We synthesize recent research developments in soil nitrogen biogeochemistry into an aspirational and accessible microbe-centered framework that clarifies understanding of nitrogen accumulation, recycling, and plant uptake processes in soil. This framework can guide scientific exploration and practical applications to boost crop yields, enrich soil organic matter, and reduce environmental nitrogen losses.