Climate change is already impacting ecosystem composition and species distributions. Here we study two different, but equally valuable New Zealand fisheries (Tasman Bay and Golden Bay, and Chatham Rise), and the potential impacts of climate change on ecosystem structure. We use mizer, a size-based multispecies modelling package, to simulate interacting fish species in each ecosystem. 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 biomasses closely matching past observations. We then carry out a controlled warming simulation experiment, allowing for temperature to remain steady or to increase for both ecosystems, both with and without fishing pressure. The shallower ecosystem of Tasman and Golden Bay has more thermally-tolerant species and experiences an overall increase in community biomass under warming, whilst the deeper ecosystem of Chatham Rise suffers an overall decline. In addition, fishing has a stronger negative impact on the Chatham Rise community. Smaller bodied animals also tend to be more resilient, both to warming and fishing impacts. Despite differences in community responses, the majority of important fisheries suffer reduced yields under warming in both ecosystems. Issues raised during the incorporation of temperature effects include species’ thermal tolerances and model calibration to data. This study facilitates ecosystem intercomparisons under climate change and offers insight into drivers of ecosystem responses.