Although nitrogen (N) availability is a major determinant of ecosystem properties, little is known about the ecological importance of plants' preference for ammonium versus nitrate (beta) for ecosystem functioning and the structure of communities. We modeled this preference for two contrasting ecosystems and showed that beta significantly affects ecosystem properties such as biomass, productivity, and N losses. A particular intermediate value of beta maximizes the primary productivity and minimizes mineral N losses. In addition, contrasting beta values between two plant types allow their coexistence, and the ability of one type to control nitrification modifies the patterns of coexistence with the other. We also show that species replacement dynamics do not lead to the minimization of the total mineral N pool nor the maximization of plant productivity, and consequently do not respect Tilman's R* rule. Our results strongly suggest in the two contrasted ecosystems that beta has important consequences for ecosystem functioning and plant community structure.