Sudden losses to food production (that is, shocks) and their consequences across land and sea pose cumulative threats to global sustainability. We conducted an integrated assessment of global production data from crop, livestock, aquaculture and fisheries sectors over 53 years to understand how shocks occurring in one food sector can create diverse and linked challenges among others. We show that some regions are shock hotspots, exposed frequently to shocks across multiple sectors. Critically, shock frequency has increased through time on land and sea at a global scale. Geopolitical and extreme-weather events were the main shock drivers identified, but with considerable differences across sectors. We illustrate how social and ecological drivers, influenced by the dynamics of the food system, can spill over multiple food sectors and create synchronous challenges or trade-offs among terrestrial and aquatic systems. In a more shock-prone and interconnected world, bold food policy and social protection mechanisms that help people anticipate, cope with and recover from losses will be central to sustainability. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.