The consequences of climate change for marine organisms are now well-known, and include metabolism and behavior modification, distribution area shifts and changes in the community. In the Bay of Biscay, the potential environmental niches of subtropical non-indigenous species (NIS) are projected to expand as a response to sea temperature rise by the mid-century under the RCP8.5 climate change scenario. In this context, this study aims to project the combined effects of changes in indigenous species distribution and metabolism and NIS arrivals on the functioning of the Bay of Biscay trophic network. To do this, we created six different Ecopath food web models: a “current situation” trophic model (2007–2016) and five “future” trophic models. The latter five models included various NIS biomass combinations to reflect different potential scenarios of NIS arrivals. For each model, eight Ecological Network Analysis (ENA) indices were calculated, describing the properties of the food web resulting from the sum of interactions between organisms. Our results illustrate that rising temperature increases the quantity of energy passing through the system due to increased productivity. A decrease in the biomass of some trophic groups due to the reduction of their potential environmental niches also leads to changes in the structure of the trophic network. The arrival of NIS is projected to change the fate of organic matter within the ecosystem, with higher cycling, relative ascendency, and a chain-like food web. It could also cause new trophic interactions that could lead to competition and thus modify the food-web structure, with lower omnivory and higher detritivory. The combined impacts (increasing temperatures and NIS arrivals) could lower the resilience and resistance of the system.