Climate change can impact marine ecosystems through many biological and ecological processes. Ecosystem models are one tool that can be used to simulate how the complex impacts of climate change may manifest in a warming world. In this study, we used an end-to-end Atlantis ecosystem model to compare and contrast the effects of climate-driven species redistribution and projected temperature from three separate climate models on species of key commercial importance in the California Current Ecosystem. Adopting a scenario analysis approach, we used Atlantis to measure differences in the biomass, abundance, and weight at age of pelagic and demersal species among six simulations for the years 2013-2100 and tracked the implications of those changes for spatially defined California Current fishing fleets. The simulations varied in their use of forced climate-driven species distribution shifts, time-varying projections of ocean warming, or both. In general, the abundance and biomass of coastal pelagic species like Pacific sardine (Sardinops sagax) and northern anchovy (Engraulis mordax) were more sensitive to projected climate change, while demersal groups like Dover sole (Microstomus pacificus) experienced smaller changes due to counteracting effects of spatial distribution change and metabolic effects of warming. Climate-driven species distribution shifts and the resulting changes in food web interactions were more influential than warming on end-of-century biomass and abundance patterns. Spatial projections of changes in fisheries catch did not always align with changes in abundance of their targeted species. This mismatch is likely due to species distribution shifts into or out of fishing areas and emphasizes the importance of a spatially explicit understanding of both climate change effects and fishing dynamics. We illuminate important biological and ecological pathways through which climate change acts in an ecosystem context and end with a discussion of potential management implications and future directions for climate change research using ecosystem models.