Seabirds are powerful environmental modulators, generating major changes in soil properties and vegetation in areas where their breeding colonies are established. One of the largest yellow-legged gull colonies in the world is found in the Atlantic Islands of Galicia National Park. In this study, we performed seasonal monitoring, over a period of 5 years, of the flora and soil in eight subcolonies characterized by different densities of gulls. Soil nutrient concentrations differed significantly between the control site and the subcolonies, as well as between seasons; the concentrations of N-NO₃^– and bioavailable P were highest in samples obtained at the end of the breeding season. Principal Component Analysis (PCA) transformed the environmental variables into three main components following varimax rotation. The PCA components were used as potential predictors in distance-based Redundancy Analyses (db- RDA) to explain turnover and also nestedness patterns in plant assemblages. Species turnover was explained by both natural (salinity) and nutrient gradients, while none of the relationships were significant in the nestedness analysis. Floristics inventories clearly revealed ruderalization of vegetation in the densest subcolonies, which led to total replacement of the most representative vascular plant species by eutrophic and ruderal species. PERMANOVA analysis showed that seagull density in 1991, when the seagull population was at its highest, could be used to group similar plant assemblages; however, this relationship was not observed for seagull density in 2011, which was 70–90% lower than in 1991. The study findings indicate that the environmental effects of seabird colonies are long lasting and that disappearance of the birds does not lead to restoration of the previous vegetation. The gull colony has irreversibly transformed the soil and vegetation of cliffs, generating a new environmental system.