© 2017 Taylor & Francis. Studies of coffee agroecosystems have focused on their role in providing habitat for biodiversity across a range of management intensities. These studies have not taken into account the temporal and spatial transformations in coffee landscapes and their impacts on structural heterogeneity and biodiversity, nor systematically linked these transformations to farmer management responses to price and policy shocks. We utilize a coupled natural–human system framework to examine the historical transformations of the coffee landscape in a matrix of community-protected forests in a coffee-growing community in Oaxaca, Mexico, and study how those transformations impact tree biodiversity across a range of management options, including formerly certified organic and conventional coffee, abandonment, and conversion. The coffee landscape has historically transitioned from forests and fields (1950s–1960s) to one dominated by coffee (1970s–1980s) to a richly mosaic and biodiverse landscape (1990–2010) resulting from 43% recent abandonment and conversion of coffee back to forest and fields.