Existing methods that apply the planetary boundary for the nitrogen cycle in life cycle assessment are spatially generic and use an indicator with limited environmental relevance. Here, we develop a spatially resolved method that can quantify the impact of nitrogen emissions to air, soil, freshwater or coastal water on “safe operating space” (SOS) for natural soil, freshwater and coastal water. The method can be used to identify potential “planetary boundary hotspots” in the life cycle of products and to inform appropriate interventions. The method is based on a coupling of existing environmental models and the identification of threshold and reference values in natural soil, freshwater and coastal water. The method is demonstrated for a case study on nitrogen emissions from open-field tomato production in 27 farming areas based on data for 199 farms in the year 2014. Nitrogen emissions were modelled from farm-level data on fertilizer application, fuel consumption and climate- and soil conditions. Two sharing principles, “status quo” and “gross value added”, were tested for the assignment of SOS to 1¿t of tomatoes. The coupling of models and identification of threshold and reference values resulted in spatially resolved characterization factors applicable to any nitrogen emission and estimations of SOS for each environmental compartment. In the case study, tomato production was found to range from not transgressing to transgressing its assigned SOS in each of the 27 farming areas, depending on the receiving compartment and sharing principle. A high nitrogen use efficiency scenario had the potential to reverse transgressions of assigned SOS for up to three farming locations. Despite of several sources of uncertainty, the developed method may be used in decision-support by stakeholders, ranging from individual producers to global governance institutions. To avoid sub-optimization, it should be applied with methods covering the other planetary boundaries.