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To feed the world population while mitigating pressing nitrogen (N) pollution problems, tremendous efforts have been devoted to developing and implementing N‐efficient technologies in crop or livestock production, but limited progress has been made. The N management improvement on a farm does not necessarily translate to N pollution reduction on a broader scale due to complex responses of natural and human systems and lack of coordination among stakeholders. Consequently, it is imperative to develop an N management framework that encompasses the complex N dynamics across systems and spatial scales, yet simple enough to guide policies and actions of various stakeholders. Here, we propose a new framework,CAFE, that defines four N management systems (Cropping,Animal‐crop,Food, andEcosystem) in a hierarchical manner, and apply it to 13 representative countries to partition N surpluses across systems in a simple and consistent manner, thereby facilitating the identification and prioritization of systems‐based intervention strategies. Surprisingly, theCropping system contributes less than half of the total N surplus within itsEcosystem for most countries, highlighting the importance of N management beyond croplands. This framework reveals that the relevant priorities and key stakeholders for enhanced N management vary among countries, such as improving theCropping‐system efficiencies in China, adjusting the animal‐crop portfolio in the Netherlands, reducing food wastage in the U.S., and lowering crop storage losses and increasing overall production capacities in African countries. As N surplus increases along theCAFEhierarchy, systems‐based intervention strategies are revealed: (a) coupling chemical fertilizers with other N sources by maintaining half of the N from manure and biological N fixation; (b) coupling animal‐crop production by reducing animal density to lower than 1.2 livestock units per hectare, and increasing self‐sufficiency of animal feed to above 50%; (c) coupling food trade with domestic demand and production; and (d) coupling population needs for economic opportunities with environmental capacity of the region. This novel framework can help unpack the “wicked” N management challenges across systems to provide new insights and tools for improving N management on and beyond farms.