Human activities are altering biodiversity and the nitrogen (N) cycle, affecting terrestrial carbon (C) cycling globally. Only a few specialized bacteria carry out nitrification—the transformation of ammonium (NH 4 + ) to nitrate (NO 3 − ), in terrestrial ecosystems, which determines the form and mobility of inorganic N in soils. However, the control of nitrification on C cycling in natural ecosystems is poorly understood. In an ecosystem experiment in the Patagonian steppe, we inhibited autotrophic nitrification and measured its effects on C and N cycling. Decreased net nitrification increased total mineral N and NH 4 + and reduced NO 3 − in the soil. Plant cover (P < 0.05) and decomposition (P < 0.0001) decreased with inhibition of nitrification, in spite of increases in NH 4 + availability. There were significant changes in the natural abundance of δ15N in the dominant vegetation when nitrification was inhibited suggesting that a switch occurred in the form of N (from NO 3 − to NH 4 + ) taken up by plants. Results from a controlled-condition experiment supported the field results by showing that the dominant plant species of the Patagonian steppe have a marked preference for nitrate. Our results indicate that nitrifying bacteria exert a major control on ecosystem functioning, and that the inhibition of nitrification results in significant alteration of the C cycle. The interactions between the C and N cycles suggest that rates of C cycling are affected not just by the amount of available N, but also by the relative availability for plant uptake of NH 4 + and NO 3 − .