Scale transition theory is a framework for predicting regional population dynamics from local process functions and estimates of spatial heterogeneity. Using this framework, we estimated regional scale functional responses for a benthic predator–prey system in the Baltic Sea. Functional responses were based on laboratory experiments or field observations of stomach contents, and prey densities measured at a local scale (0.1 m2) or a regional scale (300 km2). Laboratory data overestimated consumption at high prey densities, whereas predictions based on local scale data tallied closely with consumption observed at the regional scale. The predicted regional functional response was different for increasing and decreasing prey densities, reflecting that predator and prey densities, as well as the covariance between them, exhibit oscillatory dynamics. We conclude that it is important to validate laboratory data with small-scale field observations and that scale transition is a powerful tool for scaling-up process functions in heterogeneous systems.