The effects of fertilization on fungal plant pathogens in agricultural soils have been studied extensively. However, we know little about how fertilization affects the relative abundance and richness of soil fungal plant pathogens in natural ecosystems, either through altering the soil properties or plant community composition. Here, we used data from a seven-year nitrogen (N) addition experiment in an alpine meadow on the Qinghai-Tibetan Plateau to test how N addition affects the relative abundance and richness of soil fungal plant pathogens, as determined using Miseq sequencing of ITS1 gene biomarkers. We also evaluated the relative importance of changes in soil properties versus plant species diversity under N addition. Using general linear model selection and a piecewise structural equation model, we found that N addition increased the relative abundance of soil fungal plant pathogens by significantly altering soil properties. However, higher host plant species richness led to higher soil fungal plant pathogen richness, even after excluding the effects of N addition. We conclude that the relative abundance and richness of soil fungal plant pathogens are regulated by different mechanisms in the alpine meadow. Continuous worldwide N inputs (through both fertilizer use and nitrogen deposition) not only cause species losses via altered plant species interactions, but also produce changes in soil properties that result in more abundant soil fungal plant pathogens. This increase in pathogen relative abundance may seriously threaten ecosystem health, thus interrupting important ecosystem functions and services.