Roots concentrated on the smallest distal branching orders have short life spans and thus dominate root mortality, and may contribute predominately to plant carbon and nutrient transfer into soil. Yet the effects of nitrogen (N) enrichment on decomposition of the finest root branching orders have not yet been examined. Resolving such N effects is critical for predicting the ecosystem consequences of increased anthropogenic N deposition. The first four root orders were separated into two classes: first- and second-order roots; third- and fourth-order roots. We studied the effects of N addition on decomposition of different root order classes in four temperate tree species over 4 years. Asymptotic decay models best fit the decomposition and allowed us to examine effects of N on initial versus later stages of decomposition separately. Very early in decomposition, N fertilization stimulated decomposition rates in higher-order roots, but had no effects on initial rates of decomposition in lower-order roots. In contrast, later in decomposition, N fertilization inhibited decomposition, ultimately resulting in a larger, slowly decomposing fraction in both lower-order and higher-order roots. Inhibitory effects of N addition on lignin-degrading enzyme activity might be an important mechanism explaining the negative effects of N on decomposition here. This study highlights the importance of long-term studies for understanding N effects on decomposition, and suggests that contrasting effects of N on different decomposition processes and carbon pools should be widely considered in biogeochemical models. Furthermore, the inhibitory effects of elevated atmospheric N deposition on decomposition of lower-order roots suggest that these roots may provide a critical mechanism of carbon and nutrient retention in soil because of their rapid input via root mortality.