Agriculture accounts for approximately 10% of global greenhouse gas emissions and is simultaneously associated with impacts on human health through food consumption, and agricultural air pollutant emissions. These impacts are often quantified separately, and there is a lack of modelling tools to facilitate integrated assessments. This work presents a new model that integrates assessment of agricultural systems on (i) human health indirectly through dietary, obesity and malnutrition health risks from food consumption, (ii) human health directly through exposure to air pollutants from agricultural emissions, and (iii) greenhouse gas emissions. In the model, national food demand is the starting point from which the livestock and crop production systems that meet this are represented. The model is applied for 2014–2018 to assess the robustness of the GHG emissions and health burden results that this integrated modelling framework produces compared to previous studies that have quantified these variables independently. Methane and nitrous oxide emissions globally in 2018 were estimated to be 129 and 4.4 million tonnes, respectively, consistent with previous estimates. Agricultural systems were also estimated to emit 44 million tonnes of ammonia. An estimated 4.1 million deaths were associated with dietary health risks, 6.0 million with overweight/obesity, and 730 thousand infant deaths from malnutrition, consistent with previous studies. Agricultural air pollutant emissions were estimated to be associated with 537 thousand premature deaths attributable to fine particulate matter (PM2.5) exposure, and 184 thousand premature deaths from methane-induced ground-level ozone. These health impacts provide substantial opportunities to design integrated strategies that mitigate climate change, and improve human health, and also highlight possible trade-offs that the expansion of agricultural production could have due to increased emissions. The model presented here provides for the consistent evaluation of the implications of different agricultural strategies to meet food demand while minimising human health and climate change impacts.