The aim of this study was to investigate the influence of R. rugosa invasion on soil physicochemical and microbial properties of coastal sand dunes. The study was performed at 25 paired invaded-native plots along the Hel Peninsula at the coast of the Baltic Sea. A number of soil physicochemical and microbial parameters were measured, namely organic matter layer thickness, pH, electrical conductivity, organic C, total Ca, N, Na, P, N-NH4, N-NO3 and P-PO4 concentrations, phospholipid and neutral fatty acid (PLFA, NLFA) markers of total microbial, bacterial, fungal biomass and microbial community structure, as well as arbuscular mycorrhizal fungi (AMF) spore and species numbers, and the degree of AMF root colonization. Since potential alterations in soil parameters induced by R. rugosa may be related to large amounts of secondary metabolites provided to the soil with litter or root exudates, total phenolic concentration in senescing tissues of R. rugosa and native species was compared. Rosa rugosa invasion was associated with increased organic C, total N and P-PO4 concentrations in mineral soil relative to native vegetation. Organic matter layer under R. rugosa was thicker, had higher pH and Ca concentration. Rosa rugosa invasion was associated with reduced total microbial, bacterial and G+ bacterial biomass and increased AMF biomass markers (16:1ω5 NLFA and 16:1ω5 NLFA/PLFA), and changes in microbial community structure in mineral soil. The reduction in total and bacterial biomass under R. rugosa might have been related to the production of secondary metabolites as total phenolic concentration was approx. 5 times higher in senescing tissues of R. rugosa than in native vegetation. The observed increase in element concentrations and alterations in microbial community structure suggest that invasion of R. rugosa may threaten nutrient-poor habitats of coastal dunes. Changes in the soil environment may hinder restoration of these valuable habitats after invader removal. Display omitted •Influence of invasive Rosa rugosa on soil properties of coastal dunes was studied.•R. rugosa increased organic C, total N and P-PO4 in soil relative to native species.•Total microbial and bacterial biomass was decreased under R. rugosa.•A marker of arbuscular mycorrhizal fungi – NLFA 16:1ω5 – increased due to invasion.•Changes in soil might have been caused by high phenolic content in R. rugosa tissues.