Though human-modified tropical landscapes are increasingly well studied, the processes that influence and govern biodiversity outcomes, especially in commodity production landscapes (e.g., coffee, rubber, arecanut), remain poorly understood. A review of the existing literature reveals that research in general focuses on individual components of a cascading set of relationships from political and economic forces, to producer decisions, to agroforestry structure, to habitat and diversity. The linkages between these components remains underdeveloped; efforts to unite the full "chain of explanation" remains elusive, making it difficult to form firm claims or testable hypotheses about how the ecology and biodiversity of such commodity systems are determined. To form more robust hypotheses about such relationships would require more integrative team efforts than heretofore have been common. Our review suggests that though some important relationships are well-understood, and some emerging policy emphases can be identified, policy-relevant science is still on the horizon in this frontier area.