Permanent tree crop agriculture and multi-strata agroforestry are among the most promising options for the agricultural use of the mostly nutrient-poor and physically fragile soils of central Amazonia. In general, though, information on the optimum management of local tree crops under these conditions is inadequate. Annatto (Bixa orellana) is a small tree of tropical American origin whose seeds contain a non-toxic, carotenoid dye that is used widely in food and cosmetic products. The authors studied seed yields at ages four to seven years, biomass at seven years, nutrient accumulation and mineral nutrition of annatto trees growing in multi-strata agroforestry with different inputs of fertilizer and lime on a xanthic Ferralsol in central Amazonia. Leaf samples of three age classes were collected four times during one year, and nutrient concentrations were related to soil nutrient status, growth and yield of the trees in order to develop an optimum sampling scheme for foliar analysis. Growth and yields of the trees showed a pronounced response to increased fertilizer and lime input, which seemed to be due mainly to improved availability of phosphorus. Nitrogen fertilizer had no effect and may not be necessary for well-established trees on this soil. High litter quality and substantial nutrient recycling with annual pruning make annatto a valuable component for agroforestry systems. In this experiment, however, yields were low and decreased after the fifth year, presumably as an effect of infertile soil, shading by larger trees and, possibly, a negative effect of the drastic annual pruning with removal of the entire leaf and small-branch biomass on the vitality of the trees. Annatto is probably best suited for associations with small tree crops. Less drastic pruning treatments than those practiced in this experiment may be preferable.