Biodiversity loss is a global concern, and agriculture is one of the economic sectors responsible for this impact. The assessment of ecosystems under the influence of livestock production is essential for knowing their integrity and ability to provide ecosystem services. The aim of this investigation was to evaluate the application of LEAP/FAO guidelines for quantitative assessment of biodiversity in the livestock sector at the local scale (farm level) in a group of six study cases in Uruguay. A set of 20 indicators was used, including seven key thematic issues: habitat protection, habitat change, wildlife conservation, invasive species, pollution, aquatic biodiversity, off-farm feed, and landscape-scale conservation. The results show that the LEAP biodiversity assessment guidelines can be useful to characterize the state of ecosystems under pastoral use and some specific components of their biodiversity, as well as assess the interaction of the production system with the environment and plan management accordingly. This work also provides an analysis of the methodology used and recommendations to facilitate its application by the sector. The results from the application of the indicators show a great deal of wild biodiversity that uses grazing systems based on native grasslands as habitats and the acceptable integrity of these ecosystems. On average, farms have 83% of their native ecosystem, with a value of 3.5 for the Ecosystem Integrity Index. In terms of the richness of different groups, there was an average number of species of 112 herbaceous plants, 48 woody plants, 48 spiders, 150 birds, and 14 fish. The main goal of this work is to help in the wider application of the guidelines by facilitating decisions about methodology, necessary resources, and technical support. Moreover, another goal is to show the importance of native grasslands-based livestock systems for biodiversity conservation.