The prevalence and intensity of marine heatwaves is increasing globally, disrupting local environmental conditions. The individual and population-level impacts of prolonged heatwaves on marine species have recently been demonstrated, yet whole-ecosystem consequences remain unexplored. We compare ecosystem models parameterized before and after the onset of recent heatwaves to evaluate the cascading effects on ecosystem structure and function in the Northeast Pacific Ocean. While the ecosystem-level contribution, as prey, and demand, as predators, of most functional groups changed, gelatinous taxa experienced the largest transformations, underscored by the arrival of northward-expanding pyrosomes. Despite altered trophic relationships and energy flux, the post-heatwave ecosystem appears stable, suggesting a shift to a novel ecosystem state, with potentially profound consequences for ecosystem structure, energy flows, and threatened and harvested species.