Urbanization reshapes agricultural systems through labor and land-use changes, interacting with modernization processes including farm size expansion, mechanization, and irrigation to drive nonlinear trends in cropland nitrogen use. Using a 61-year dataset from 139 countries, here we show that the association between urbanization and nitrogen outcomes is profoundly nonlinear and contingent on development stages. In low-income countries, urbanization initially increases fertilizer use while suppressing nitrogen yield and efficiency, though larger farm sizes mitigate these early losses. As countries reach upper-middle-income levels, modernization enhances nitrogen efficiency but introduces trade-offs between environmental gains and yield growth. In high-income countries, advanced modernization mitigates adverse urban impacts, reversing nitrogen use efficiency from a 4% decline to a 12% gain at high urbanization levels. These findings indicate that there is no universal sustainability pathway. Instead, integrating land consolidation, mechanization, and precision irrigation can transform urbanization into a catalyst for sustainable management and resilient food systems.