Under climate change, species composition and abundances in high-latitude waters are expected to substantially reconfigure with consequences for trophic relationships and ecosystem services. Outcomes are challenging to project at national scales, despite their importance for management decisions. Using an ensemble of six global marine ecosystem models we analyzed marine ecosystem responses to climate change from 1971 to 2099 in Canada’s Exclusive Economic Zone (EEZ) under four standardized emissions scenarios. By 2099, under business-as-usual emissions (RCP8.5) projected marine animal biomass declined by an average of −7.7% (±29.5%) within the Canadian EEZ, dominated by declines in the Pacific (−24% ± 24.5%) and Atlantic (−25.5% ± 9.5%) areas; these were partially compensated by increases in the Canadian Arctic (+26.2% ± 38.4%). Lower emissions scenarios projected successively smaller biomass changes, highlighting the benefits of stronger mitigation targets. Individual model projections were most consistent in the Atlantic and Pacific, but highly variable in the Arctic due to model uncertainties in polar regions. Different trajectories of future marine biomass changes will require regional-specific responses in conservation and management strategies, such as adaptive planning of marine protected areas and species-specific management plans, to enhance resilience and rebuilding of Canada’s marine ecosystems and commercial fish stocks.