Reactive nitrogen (N) deposition can affect ecosystem processes, particularly in oligotrophic upland habitats. Phosphorus (P) addition has been proposed to reduce the effects of N enrichment on N leaching and acidification, since P limitation can reduce biomass production and consequent sequestration of reactive N. However, biodiversity is often reduced in more productive ecosystems and P limitation may protect against this effect. Responses to P availability in instances of high N deposition are poorly understood. This study investigated the ecosystem response to alleviation of P limitation, using a long-term nutrient addition experiment (1996–2012) three years after ceasing N inputs and 15years after a single P application. Substantial differences were observed in the structure and composition of vegetation species and above-ground vegetation biomass. Vegetation height was greater in the N+P addition treatments (+38% cf. control), with increased cryptogam cover (+47%), whereas N addition increased graminoid species cover (+68%). Vegetation diversity was significantly reduced by the addition of P (−21%), indicating that P limitation is likely to be an important mechanism that limits biodiversity loss in upland habitats exposed to chronic N deposition. Significant differences in soil C and N contents were also observed between treatments. Relative to control, the addition of N increased soil C (+11%) and N (+11%) pool sizes, whereas the addition of N and P reduced soil C (−12%) and N (−13%) pool sizes. This demonstrated the importance of P availability for upland ecosystem processes, and highlights the long-term effects of P addition on vegetation species composition and C storage. Thus, the addition of P cannot be endorsed as a method for reducing impacts of N deposition.Capsule: Phosphorus limitation is a major mechanism governing ecosystem processes in situations of high atmospheric nitrogen deposition.