The Body Condition Score (BCS) protocol is a non-invasive method for assessing and collecting health data without disturbing the animals being studied. The primary goal of BCS is to categorize the amount of body fat in different body parts into different scores that reflect an individual animal’s nutritional status. This status can fluctuate throughout an animal’s life due to various factors, including food availability, seasonal hormonal changes, age, and reproductive condition. In this study, we evaluated the effectiveness of this approach in analyzing the BCS dynamics of lowland tapirs (Tapirus terrestris) living in two Brazilian biomes: the Cerrado and the Pantanal. These biomes are distinguished by their unique vegetation structures, seasonal variations, and levels of exposure to human-induced threats. We specifically tested how the BCS varies across biomes, health conditions, age stages, and seasonal changes by systematically comparing these factors in tapirs between these biomes. Our findings indicate that the BCS is not effective at capturing predicted differences in health and sex among lowland tapirs within biomes. However, it is a practical method for examining differences among tapirs in the Cerrado and Pantanal biomes. In the Pantanal region, tapirs showed no significant differences in BCS due to variations in wet and dry conditions, but the results suggest that female tapirs generally have a lower BCS than males. We discuss how the BCS approach can be a tool for monitoring wildlife health and the importance of interpreting its results with caution, particularly for projects that lack resources for a comprehensive health investigation. Moving forward, integrating various methods—such as clinical visual inspections, genetic analyses, and habitat assessments—alongside traditional BCS evaluations could offer a more comprehensive understanding of the health and conservation needs of tapirs and other vertebrate species.