Increased animal productivity has reduced animal fitness, resulting in increased susceptibility to infectious and metabolic diseases, locomotion problems and subfertility. Future animal breeding strategies should focus on balancing high production levels with health status monitoring and improved welfare. Additionally, understanding how animals interact with their internal and external environment is essential for improving health, fitness, and welfare. In this context, the continuous validation of existing biomarkers and the discovery and field implementation of new biomarkers will enable us to understand the specific physiological process and regulatory mechanisms used by the organism to adapt to different environmental conditions. Thus, biomarkers may be used to monitor welfare and improve management and breeding strategies. In this article, we describe major achievements in the establishment of biomarkers in dairy cows and small ruminants. This review mainly focuses on the physiological biomarkers used to monitor animal responses to, and recovery from, environmental perturbations. We highlight future avenues for research in this field and present a timely positioning document to the scientific community.