Understanding how climate regulates trophic control may help to elucidate the causes of transitions between alternate ecosystem states following climate regime shifts. We used a 34-year time series of the abundance of Pacific cod (Gadus macrocephalus) and five prey species to show that the nature of trophic control in a North Pacific ecosystem depends on climate state. Rapid warming in the 1970s caused an oscillation between bottom–up and top–down control. This shift to top–down control apparently contributed to the transition from an initial, prey-rich ecosystem state to the final, prey-poor state. However, top–down control could not be detected in the final state without reference to the initial state and transition period. Complete understanding of trophic control in ecosystems capable of transitions between alternate states may therefore require observations spanning more than one state.