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Food security, climate change mitigation, and land use challenges are interlinked and need to be considered simultaneously. One possible solution is sustainable intensification, which is the practice of increasing food production per area of land whilst also reducing the environmental impacts associated with this. Agroforestry has been stated to be a practice that meets this definition. In this study, a new methodology is presented to assess the potential of different management options as sustainable intensification practices. The methodology is based on comparing the carbon emissions associated with the production of food and the carbon sequestered for that same activity for a particular quantity of food produced over a specific area and over a specific time. The resulting indicator, the "carbon balance" is the difference between the greenhouse gasses emitted (considered as negative values) and carbon sequestered (positive values) estimated in Mg CO2eq per Mg of food produced on one hectare of land for one year. The carbon balance quantifies the global warming potential associated with sustainable intensification by integrating a process-based model with life cycle analysis and is able to estimate above- and below-ground biomass and soil carbon content. This methodology is tested in Portugal for wheat production under crop monoculture and agroforestry systems. The results show agroforestry to be a suitable practice for sustainable intensification compared to a crop monoculture as it just slightly decreased wheat yields whilst providing a positive carbon balance from year 50 onwards of approximately 1 Mg of CO2eq sequestered per Mg of wheat produced.