Emissions of nitrous oxide (N2O) and nitric oxide (NO) from agricultural soils in the tropics are important in the global budgets of these trace gases. We made monthly measurements of N2O and NO emissions from pastures with three different management systems on volcanic soils in northwestern Costa Rica: traditional (no N input from fertilizer or legumes), pastures with a grass-legume combination, and pastures fertilized with 300 kg N ha−11 yr−1. Average annual N2O emissions were 2.7 ng N cm−2 h−1 from the traditional pastures, 4.9 ng N cm−2 h−1 from the grass-legume pastures, and 25.8 ng N cm−2 h−1 from the fertilized pastures. Average annual NO emissions were 0.9, 1.3, and 5.3 ng N cm−2 h−1 from traditional, grass-legume and fertilized pastures, respectively. In a separate experiment the effects of ammonium, nitrate, and urea-based fertilizer mixtures on nitrogen oxide fluxes were compared. We measured nitrogen oxide fluxes following four different fertilization events. Nitrogen oxide fluxes were among the highest ever measured. The difference in soil water content between the fertilization events had a far greater effect on N2O and NO emissions than the effect of fertilizer composition. We conclude that the concept of “emission factors” for calculating N2O and NO emissions from different types of N fertilizer is flawed because environmental factors are more important than the type of N fertilizer. To estimate fertilizer-induced N2O emission in tropical agriculture, stratification according to soil moisture regime is more useful than stratification according to fertilizer composition.