Rosa rugosa Thunb. (Japanese Rose) is one of the most invasive species in Europe. It spreads spontaneously in coastal areas of western, central and northern Europe, posing a threat to dune habitats, including those indicated in the EU Habitats Directive as particularly valuable. R. rugosa has already been reported to displace native plants and alter soil properties. However, little is known about how these effects are mediated by the habitat context or the invader condition (health, ontogenetic stage). This study addressed that gap by examining vegetation and soil in 22 R. rugosa-invaded sites, half of which were in yellow dunes and the other half in grey dunes, i.e. two habitats representing the earlier and later stages of dune succession. The study was conducted on the Hel Peninsula (Poland’s Baltic coast). R. rugosa had a significant impact on dune vegetation, but the impact was strongly dependent on the habitat type. In the yellow dune sites, R. rugosa outcompeted most resident plant species, which translated into a strong decline in their total cover and richness. The invasion was almost not accompanied by changes in soil properties, suggesting that it affected the resident vegetation directly (through space takeover and shading). In the grey dunes, R. rugosa caused a shift in species composition, from that characteristic of open communities to that typical of forests. In this habitat, a significant increase in the soil organic layer thickness under R. rugosa was also observed, which means that both direct and indirect effects of the invasion on the vegetation should be assumed. Finally, a negative relationship was found between the total chlorophyll content in R. rugosa leaves and the parameters of resident plant communities, showing that the invasion effects can vary not only across habitats, but also with the condition of the invader. The results may have practical implications for managing R. rugosa invasions in coastal sand dune systems. Since R. rugosa accelerates grey dune succession, protecting this habitat may be more urgent and, at the same time, more complicated than protecting dunes at the earlier stages of development.