The cessation of seal harvesting has prompted a recovery of previously decimated fur seal (Arctocephalus gazella and Arctocephalus tropicalis) populations across the Southern Ocean region. Although the associated increase in seal-related soil disturbance is known to impact indigenous vegetation, the effect of increasing fur seal numbers on exotic plant species is not yet clear. Here, we compare plant species composition and cover between 26 sites with high fur seal impact paired with nearby control sites on sub-Antarctic Marion Island. Seal-affected sites had a significantly higher number and cover of exotic plants, specifically of the widespread sub-Antarctic invaders, Poa annua and Sagina procumbens, than control sites. Furthermore, some of the native species, most notably the disturbance-sensitive species, Blechnum penna-marina, were significantly less abundant in seal-affected sites compared to controls. We propose that this is a result of both physical trampling, which opens up niches for exotics by damaging natives, and nutrient enrichment of the soils, giving exotic species a competitive advantage over natives. While other studies have noticed associations between exotic plant species and indigenous animal disturbance, this is, to the best of our knowledge, the first study to empirically show that the successful recovery of fur seal populations can have undesirable side-effects such as the enhanced persistence of exotic plant species. We recommend that alien plant management plans specifically include areas of increased animal disturbance into their programmes.