The risks imposed by biological invasions on marine ecosystems are increasing worldwide. The mud crab Rhithropanopeus harrisii has recently expanded its distribution to the northeastern Baltic Sea, where low predatory pressures and the absence of functionally similar competitors favored the establishment of the species. Few studies have addressed the effects of the mud crab on Baltic benthic communities and habitats. Even fewer have looked at the consequences of the invader on habitats dominated by Fucus vesiculosus, the main habitat-forming macrophyte in the Baltic Sea. The present study experimentally analyzed, under laboratory conditions, the effects of R. harrisii on Baltic F. vesiculosus habitats and associated communities under different temperatures simulating summer and winter regimes. Our results show that the effects of the mud crab are modulated by temperature, being more pronounced under summer conditions when the metabolic demands and food intake requirements are higher. The experiment provided new insights into the capacity of R. harrisii to disrupt recruitment in native snail populations, jeopardizing the persistence of healthy populations of key grazers in F. vesiculosus habitats. Moreover, our results conclusively demonstrated the capacity of the invader to decimate native blue mussel populations. The impacts on functionally relevant invertebrates can have far-reaching ecological consequences, altering the food web and disrupting entire coastal ecosystems in the Baltic Sea.