The Chocolate Tree chronicles the natural and cultural history of Theobroma cacao and explores its ecological niche. Tracing cacao's "journey" out of the rain forest, into pre-Columbian gardens, and then onto plantations adjacent to rain forests, Allen M. Young describes the production of this essential crop, explaining how the seeds are extracted from the large, colorful pods.

He details the environmental price of Europeanized cultivation, and ways that current reclamation efforts for New World rain forests can improve the natural ecology of the cacao tree.

Recounting more than a dozen years of ecological fieldwork in and around cacao plantations in Costa Rica, Young reviews his research into the problem of poor levels of natural pollination on plantations. He recalls encounters with sloths, toucans, butterflies, giant tarantula hawk wasps, and other creatures found in cacao groves. Among these creatures Young discovered a tiny fly that provides a vital link between the chocolate tree and its original rain forest habitat.

This discovery leads him to conclude that cacao trees in cultivation today may have lost their original insect pollinators due to the plants' long history of agricultural manipulation.