The increasing presence of chemicals in food and the environment raises significant public health concerns, as chronic exposure to residues or contaminants like pesticides, heavy metals, and persistent organic pollutants (POPs) can lead to adverse health effects, even at low levels. Effect biomarkers, which indicate biological changes in response to exposure, are essential tools for assessing health risks associated with these contaminants. Unlike exposure biomarkers that detect chemical presence, effect biomarkers provide insights into biological responses, helping understanding toxicological mechanisms. This review discusses the use of effect biomarkers in food safety and environmental health, examining types, their relevance in studies, and advancements in detection techniques such as metabolomics. Two case studies are explored, highlighting varied applications and nuances in using effect biomarkers in food safety and environmental health. Finally, the review addresses the challenges and future directions for integrating effect biomarkers into regulatory science to improve chemical risk assessments and management strategies.