Climate change is already impacting ecosystem composition and species distributions. A question remains as to how future climate change will alter ecosystem structure. Here we study two distinctly different, but equally valuable New Zealand fisheries (Tasman Bay and Golden Bay, and Chatham Rise), and the potential impacts that climate change could cause. We use mizer, a size-based multispecies modelling package, to simulate a high number of interacting fish species in each ecosystem. By utilising therMizer, an extension of mizer which incorporates temperature effects on species’ metabolic rate and aerobic scope, we implement historical climate data from the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP). This enables us to recreate the historical time period of 1961–2010, deriving reasonable steady state with biomasses closely matching those observed in the past. We then simulate forwards to 2060, allowing for temperature to remain steady or to increase, and for fishing to occur, and look at the resulting changes in species biomasses. It was found that while specific species responses differ, both ecosystems generally decrease in abundance under climate change. Chatham Rise is much more impacted by fishing effects. Species with higher thermal tolerance ranges tended to fare better under climate change. Issues raised during the incorporation of temperature effects include knowledge of species’ thermal tolerances and the importance of how the initial steady state is tuned, as this has significant flow-on effects on species dynamics. This study will help advance other ecosystem models aiming to account for future climate change impacts.