The Kerguelen Plateau in the Indian sector of the Southern Ocean is a highly dynamic region for Southern Ocean ecosystems and an important region for the Patagonian toothfish fishery. Fished regions overlap with foraging regions for predators; however, no study has explored the spatial impacts of fishing on ecosystem dynamics. We developed two spatially explicit ecosystem models to (i) explore the spatial effects of fishing on the Patagonian toothfish and the ecosystem in scenarios with and without fishing; and (ii) use modelled distributions to compare ecosystem representation in Marine Protected Areas (MPAs) with existing studies. Consistent with other studies, we found decreases in Patagonian toothfish biomass in scenarios with fishing activity. In contrast, we found no spatial fishing impacts on ecosystem interactions. A majority of functional group distributions were positively correlated with phytoplankton and well distributed within no-take areas. This could indicate a high level of representation of species in MPAs. Our study provides valuable insights into spatial ecosystem dynamics on the Kerguelen Plateau; however, our interpretations were limited and more research is needed to disentangle the natural variation from fishing impacts and further explore spatio-temporal changes in phytoplankton on the ecosystem.