We used coffee farming households as units of analysis to synthetize agrobiodiversity data in agricultural plots managed by coffee cooperative members of Nicaragua and El Salvador. Surveys, focus groups and plant inventories were used to analyze agrobiodiversity and its contribution to household livelihoods. Coffee farming families managed high levels of agrobiodiversity, including shade and other trees, epiphytes, agricultural crops and medicinal plants. Individual small farms contained higher levels of agrobiodiversity compared to cooperatives managing larger landholdings collectively. Families benefited from agrobiodiversity through consumption of food, firewood, timber and medicinal. In addition, they used these products to generate income through sales. An analysis of a case study in El Salvador showed that shade tree biodiversity levels in a 35 ha collectively managed cooperative did not significantly change over 9 years. The levels of plant agrobiodiversity found in small farms and cooperatives show promise for conserving species in shade coffee. However, this will require integrated programs that not only enhance conservation activities, but also support household livelihoods.