For over three decades, Swiss agricultural soils have received substantial organic nitrogen inputs, particularly as manure. Improved manure and livestock management has reduced ammonia emissions while increasing nitrogen availability, reinforcing its central role in the national nutrient budget. Once applied, nitrogen can be taken up by crops, stored in soil organic matter, or lost through leaching and gaseous emissions. These processes are shaped by management practices (e.g. residue handling, fertiliser type) and local conditions such as soil type, rainfall, and temperature. Because the balance between the build-up and breakdown of soil organic matter changes only slowly, assessing nitrogen use efficiency requires long-term datasets. While Swiss long-term field experiments provide data on key nitrogen flows (fertiliser inputs, crop uptake, soil nitrogen stock changes), major gaps remain regarding biological nitrogen fixation and the role of crop residues. This project will combine long-term field and lysimeter data with targeted measurements, modelling and policy analysis to build science-based foundations for integrated, site-specific fertilisation strategies in Switzerland.