Ecological communities are constantly changing as a response to environmental and anthropogenic pressures. Yet, how changes in community composition influence the structure of food webs over time and space remains elusive. Using ecological network analysis, we assessed how food web structure changed across six distinct areas of the North Sea over a sixteen-year time-period. We used multivariate analyses to disentangle and compare spatio-temporal dynamics in community composition (i.e. changes in species abundances) and food web structure (i.e. changes in network properties). Specifically, we assessed how changes in community composition were reflected in food web structure. Our results revealed a strong spatial coupling between community composition and food web structure along a south–north gradient. However, the temporal covariation between community composition and food web structure depended on the spatial scale. We observed a temporal mismatch at regional scale, but a strong coupling at local scale. In particular, we found that community composition can be influenced by hydro-climatic events over large areas, with diverse effects manifesting in local food web structure. Our proposed methodological framework quantified and compared spatio-temporal changes in community composition and food web structure, providing key information to support effective management strategies aimed at conserving the structure and functioning of ecological communities in times of environmental change.