Climate change constitutes a major challenge for marine urban ecosystems and ocean warming will likely strongly affect local communities. Non-Indigenous Species (NIS) have been shown to often have higher heat resistance than natives, but studies investigating how forthcoming global warming might affect them in marine urban environments remain scarce, especially in situ studies. Here we used an in situ warming experiment in a NW Mediterranean (warm temperate) and a NE Atlantic (cold temperate) marina to see how global warming might affect recruited communities in the near future. In both marinas, warming resulted in significantly different community structure, lower biomass, and more empty space compared to control. However, while in the warm temperate marina, NIS showed an increased surface cover, it was reduced in the cold temperate one. Metabolomic analyses on Bugula neritina in the Atlantic marina revealed potential heat stress experienced by this introduced bryozoan and a potential link between heat stress and the expression of a halogenated alkaloid, Caelestine A. The present results might indicate that the effects of global warming on the prevalence of NIS may differ between geographical provinces, which could be investigated by larger scale studies.