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Nitrogen fertilization is a key factor for coffee production but creates a risk of water contamination through nitrate (NO 3 − ) leaching in heavily fertilized plantations under high rainfall. The inclusion of fast growing timber trees in these coffee plantations may increase total biomass and reduce nutrient leaching. Potential controls of N loss were measured in an unshaded coffee (Coffea arabica L.) plot and in an adjacent coffee plot shaded with the timber species Eucalyptus deglupta Blume (110 trees ha−1), established on an Acrisol that received 180 kg N ha−1 as ammonium-nitrate and 2,700 mm yr−1 rainfall. Results of the one year study showed that these trees had little effect on the N budget although some N fluxes were modified. Soil N mineralization and nitrification rates in the 0–20 cm soil layer were similar in both systems (≈280 kg N ha−1 yr−1). N export in coffee harvest (2002) was 34 and 25 kg N ha−1 yr−1 in unshaded and shaded coffee, and N accumulation in permanent biomass and litter was 25 and 45 kg N ha−1 yr−1, respectively. The losses in surface runoff (≈0.8 kg mineral N ha−1 yr−1) and N2O emissions (1.9 kg N ha−1 yr−1) were low in both cases. Lysimeters located at 60, 120, and 200 cm depths in shaded coffee, detected average concentrations of 12.9, 6.1 and 1.2 mg NO 3 − -N l−1, respectively. Drainage was slightly reduced in the coffee-timber plantation. NO 3 − leaching at 200 cm depth was about 27 ± 10 and 16 ± 7 kg N ha−1 yr−1 in unshaded and shaded coffee, respectively. In both plots, very low NO 3 − concentrations in soil solution at 200 cm depth (and in groundwater) were apparently due to NO 3 − adsorption in the subsoil but the duration of this process is not presently known. In these conventional coffee plantations, fertilization and agroforestry practices must be refined to match plant needs and limit potential NO 3 − contamination of subsoil and shallow soil water.