Rapidly spreading leguminous plantations in tropics recently have been suggested to be new important nitrous oxide (N2O) sources due to their high nitrogen (N)-fixing ability and rapid spread. We examined effects of phosphorus (P) fertilization on the N2O emissions from an Acacia mangium plantation in Indonesia by separating root-excluded plots and root-existing plots using trench method to understand roles of microbial and plant root activities in the effects separately. In root-excluded plots, P application tended to enhance N2O emissions. Higher inorganic N content in P-applied plots indicated that P application accelerated the N-cycling and stimulated nitrification and/or denitrification, thereby enhanced N2O emissions. In contrast, P application significantly reduced N2O emissions in root-existing plots, attributed to accelerated root N uptake. Inorganic N content was lower in P-applied plots. Our study suggests that P fertilizer is helpful to suppress the N2O emissions from Acacia mangium plantations but yet P fertilizer have to be used carefully, because when there is no vegetation as harvesting times P application could stimulate the N2O emissions.