Food systems are primary drivers of human and environmental health, but the understanding of their diverse and dynamic co-transformation remains limited. We use a data-driven approach to disentangle different development pathways of national food systems (i.e. ‘transformation archetypes’) based on historical, intertwined trends of food system structure (agricultural inputs and outputs and food trade), and social and environmental outcomes (malnutrition, biosphere integrity, and greenhouse gases emissions) for 161 countries, from 1995 to 2015. We found that whilst agricultural total factor productivity has consistently increased globally, a closer analysis suggests a typology of three transformation archetypes across countries: rapidly expansionist, expansionist, and consolidative. Expansionist and rapidly expansionist archetypes increased in agricultural area, synthetic fertilizer use, and gross agricultural output, which was accompanied by malnutrition, environmental pressures, and lasting socioeconomic disadvantages. The lowest rates of change in key structure metrics were found in the consolidative archetype. Across all transformation archetypes, agricultural greenhouse gases emissions, synthetic fertilizer use, and ecological footprint of consumption increased faster than the expansion of agricultural area, and obesity levels increased more rapidly than undernourishment decreased. The persistence of these unsustainable trajectories occurred independently of improvements in productivity. Our results underscore the importance of quantifying the multiple human and environmental dimensions of food systems transformations and can serve as a starting point to identify potential leverage points for sustainability transformations. More attention is thus warranted to alternative development pathways able of delivering equitable benefits to both productivity and to human and environmental health.