At least 17,000 families in Bolivia make a living from coffee farming. Around 65% of coffee is produced under different levels of shade trees in agroforestry systems, but there is a general trend towards transforming shade agroforests into full sun coffee monocultures. Shaded coffee crops not only improve the establishment and life spans of coffee plants, but also maintain crop and wild biodiversity in the landscape, and in consequence, ecosystem services (e.g. food and nutrition diversity, and pollination). High-quality coffee farms are interesting for on-farm biodiversity conservation, because their certification standard considers biodiversity as a quality indicator. However, few studies analyse the decisions that farmers make on coffee farms and the structure and composition of their coffee farms. This collaborative project between the Instituto de Ecología (IE), Bolivia, the Centre for Development and Environment (CDE) and the Institute of Geography (GIUB), both of the University of Bern, Switzerland, aims to study the contribution of specialty coffee (high quality coffee) farms in Bolivia to biodiversity conservation. It analyses farm management and the patterns of change of vegetation (i.e. botanical composition and structure) on farms. Besides insights gained, this seed-funded project will help identify broader research questions to be addressed in a larger research project. This study also helps establish a specialty coffee research network of institutions and interested stakeholders in Bolivia linked to experts in Switzerland.