This paper proposes an innovative framework to describe sustainable transitions of food systems while considering simultaneously socio-economic and environmental issues, in a just transition perspective. This framework (i) describes the structural changes needed for a sustainable transition in food systems; (ii) assess their effects on employment at the farm and processing industry level; (iii) detect the political levers needed to make this transition a just one—that is, preserving jobs and livelihoods for communities. Using the decarbonation pathway for the agricultural sector issued from the French National Low-Carbon Strategy as reference, we developed two scenarios for the French dairy sector which have the same level of climate ambitious, but a different approach to reach the target. Aiming exclusively to achieve a greenhouse gases reduction, the first scenario relies only on supply side measures. This scenario has a negative impact in terms of employment loss at the farm level and in the agri-food sector. In contrast, a multifunctional scenario considering simultaneously climate, biodiversity, health, and employment issues, and playing with policy measures targeting supply, demand and market organisation can maintain jobs in the farm and agri-food sector, contributes to restore the agro-biodiversity and develops food products compatible with healthy nutritional guidelines.