In intensive cultivation of coffee (Coffea arabica L.), large N fertilizer inputs are thought to increase nitrate (NO3 −) water contamination and greenhouse gas emissions. This study was carried out (1) to evaluate the nitrogen use efficiency of a highly fertilized C. arabica–Inga densiflora agroforestry system on an Andosol and (2) to determine the control mechanisms of N fluxes and losses. Nitrogen pools and fluxes were monitored for one cropping season in a coffee plantation (density 4,722 plants ha−1, height 2.1 m), shaded by regularly pruned leguminous trees (density 278 trees ha−1; height 8 m), in the Central Valley of Costa Rica. The fate of N fertilizer (250 kg N ha−1 year−1) was traced by adding 15N-urea at 1.61 kg 15N ha−1. The labeled urea was rapidly nitrified or immobilized in soil organic matter with 20.8 % recovered in organic form at the end of the cropping season in the top 2 m of the soil. There was high net N mineralization and nitrification in the top soil (≈200 kg N ha−1 year−1 in 0–10 cm) and up to 257 kg NO3 −–N ha−1 were found in the top 2 m of the soil. Only 25.2 % (63 kg N ha−1) of the applied fertilizer (15N recovery) was taken up by the two plant species (13.5 % in the coffee plants, 9.6 % in the shade trees and 2.1 % in the litter). Total N export in the coffee fruit harvest accounted for 110 kg N ha−1 but only 17.6 kg N ha−1 came from the applied fertilizer (7 % of 15N recovery). During this year of high coffee production, the coffee plant acquired most of its N from mineralized soil N rather than from N fertilizer. High fertilization resulted in a low rate of N2 fixation by I. densiflora, estimated at 22.7 kg N ha−1 year−1 (Ndfa of 16.1 %). As a result of high water drainage (1,745 mm for a total rainfall of 2,678 mm), the main fate of N fertilizer was NO3 − leaching (33–55 % of 15N recovery). The annual NO3 −–N leaching at a depth of 120 cm was 157.2 kg N ha−1 year−1(including 82.8 from applied N) and the N2O–N emission was 5.8 kg N ha−1 year−1. These results clearly showed that the system was N saturated, leading to low use efficiency of the N fertilizer and significant losses of N, principally through NO3 − leaching. This study provided an insight on how to reduce the negative environmental impact of N fertilization in intensive coffee cultivation and increase N use efficiency.