As a major source of greenhouse gas (GHG) emissions and with a substantial potential of carbon storage, agriculture and food (agri-food) systems play a two-fold role in achieving the Paris goal of well below 2 °C of global warming. Against this background, this paper assesses the mitigation potentials, economic effects, co-benefits and trade-offs of biophysically feasible transitions of the Austrian agri-food system. By combining biophysical accounting with a comparative-static multi-sectoral computable general equilibrium model, we assess both supply- and demand-side driven transition scenarios. These scenarios entail substantial changes in the Austrian agri-food system, mitigating between 70 and 110% of GHG emissions relative to the reference pathway in 2050, with lower emission intensities from agricultural practices and enhanced sinks through afforestation. Two out of three scenarios lead to economy-wide costs of up to 1% of gross domestic product. Despite these small changes at the macroeconomic scale, output effects within the Austrian agri-food sectors are substantial, with primary production and manufacturing of plant-based products emerging as winners in terms of sectoral revenue, while animal-based primary production and manufacturing lose. The agri-food system transitions considered create health co-benefits, but reveal trade-offs between mitigation potentials, biodiversity conservation and economic effects.