Pragmatic methods to assess the status of biodiversity at multiple scales are required to support conservation decision-making. At the intersection of several major biogeographic zones, Bolivia has extraordinary potential to develop a monitoring strategy aligned with the objectives of the Group on Earth Observations Biodiversity Observation Network (GEO BON). Bolivia, a GEO Observer since 2005, is already working on the adequacy of national earth observations towards the objectives of the Global Earth Observation System of Systems (GEOSS). However, biodiversity is still an underrepresented component in this initiative. The integration of biodiversity into Bolivia’s GEO framework would confirm the need for a country level biodiversity monitoring strategy, fundamental to assess the progress towards the 2020 Aichi targets. Here we analyse and discuss two aspects of the process of developing such a strategy: (1) identification of taxonomic, temporal and spatial coverage of biodiversity data to detect both availability and gaps; and (2) evaluation of issues related to the acquisition, integration and analyses of multi-scale and multi-temporal biodiversity datasets. Our efforts resulted in the most comprehensive biodiversity database for the country of Bolivia, containing 648,534 records for 27,534 species referenced in time and space that account for 92.5% of the species previously reported for the country. We capitalise this information into recommendations for the implementation of the Bolivian Biodiversity Observation Network that will help ensure that biodiversity is sustained as the country continues on its path of development.