The presence of carcinogenic substances in beef poses a significant risk to public health, with far-reaching implications for consumer safety and the meat production industry. Despite advancements in food safety measures, traditional breeding methods have proven inadequate in addressing these risks, revealing a substantial gap in knowledge. This review aims to fill this gap by evaluating the potential of healthy breeding techniques to significantly reduce the levels of carcinogenic compounds in beef. We focus on elucidating the molecular pathways that contribute to the formation of key carcinogens, such as heterocyclic amines (HCAs) and polycyclic aromatic hydrocarbons (PAHs), while exploring the transformative capabilities of advanced genomic technologies. These technologies include genomic selection, CRISPR/Cas9, base editing, prime editing, and artificial intelligence-driven predictive models. Additionally, we examine multi-omics approaches to gain new insights into the genetic and environmental factors influencing carcinogen formation. Our findings suggest that healthy breeding strategies could markedly enhance meat quality, thereby offering a unique opportunity to improve public health outcomes. The integration of these innovative technologies into breeding programs not only provides a pathway to safer beef production but also fosters sustainable livestock management practices. The improvement of these strategies, along with careful consideration of ethical and regulatory challenges, will be crucial for their effective implementation and broader impact.