Plant species occurrence in Europe is affected by changes in nitrogen deposition and climate. Insight into potential future effects of those changes can be derived by a model approach based on field-based empirical evidence on a continental scale. In this paper, we present a newly developed empirical model PROPS, predicting the occurrence probabilities of plant species in response to a combination of climatic factors, nitrogen deposition and soil properties. Parameters included were temperature, precipitation, nitrogen deposition, soil pH and soil C/N ratio. The PROPS model was fitted to plant species occurrence data of about 800,000 European relevés with estimated values for pH and soil C/N ratio and interpolated climate and modelled N deposition data obtained from the Ensemble meteo data set and EMEP model results, respectively. The model was validated on an independent data set. The test of ten species against field data gave an average Pearson's r-value of 0.79. PROPS was applied to a grassland and a heathland site to evaluate the effect of scenarios for nitrogen deposition and climate change on the Habitat Suitability Index (HSI), being the average of the relative probabilities, compared to the maximum probability, of all target species in a habitat. Results for the period 1930–2050 showed that an initial increase and later decrease in nitrogen deposition led to a pronounced decrease in HSI, and with dropping nitrogen deposition to an increase of the HSI. The effect of climate change appeared to be limited, resulting in a slight increase in HSI.