Nitrogen (N) is essential for agricultural productivity, but excessive N inputs result in substantial losses to the environment. Conducting N assessments at national scales is challenging because observational data are limited, especially over long time periods. Here we compiled detailed datasets and performed high-resolution biogeochemical modelling to quantify N budgets for Switzerland's diverse agricultural ecosystems over four decades, with a focus on croplands and grasslands (i.e., permanent managed meadows used for livestock feed). Between the 1980s and the 2010s, N use efficiency improved from 47 % to 57 % in croplands and from 63 % to 71 % in grasslands, while losses through leaching and gas emissions decreased by 24 % in croplands and 4 % in grasslands. These improvements are closely linked to the implementation of national-scale agri-environmental policies that reduced fertilizer use in the 1990s. However, despite increased efficiency, cropland soils experienced substantial N depletion between 1995 and 2011 (−23 ) in croplands. Our results demonstrate that policy reforms have improved agricultural system functioning and reduced losses, but also reveal risks associated with unbalanced soil N, underscoring the need for integrated N management for sustainable agriculture.