The use of nitrogen (N) in fertilizer has doubled the amount of reactive N in the biosphere, leading to increased greenhouse-gas emissions and nutrient enrichment in aquatic and terrestrial ecosystems. Despite the global impact of N, many uncertainties exist about the factors that determine the loss and retention of fertilizer-associated N in terrestrial ecosystems. A growing body of evidence shows that linkages between plants and soil microbes play a major role in controlling the loss and retention of N. The promotion of such plant–microbial linkages in agricultural systems has the potential to enhance N retention and reduce N loss. Although trade-offs with agricultural yield are inevitable, promoting plant–microbial linkages will reap benefits in terms of plant crop resistance to climate change as well as to pests and diseases.