Metagenomics, the study of genetic material directly extracted from environmental samples, has revolutionised microbial research by enabling culture-independent investigation of microbial diversity, community structure, and potential. It has become a potent tool in livestock production systems for addressing major challenges related to animal health, productivity, environmental sustainability, antimicrobial resistance, and greenhouse gas emissions. Metagenomic approaches have provided critical insights into ruminal microbial ecology, host–microbiome interactions, feed efficiency, milk production, heat stress resilience, metabolic disorders, and methane emissions, in addition to facilitating the identification of microbial biomarkers and functional pathways associated with economically important traits. Furthermore, metagenomics has improved One Health surveillance through characterization of resistomes, mobile genetic elements, zoonotic pathogens, and microbial reservoirs of antimicrobial resistance. Applications also extend to uterine and faecal microbiome research, viral detection, novel enzyme discovery, therapeutic development, and biodegradation. The use of metagenomics in precision nutrition, microbiome-informed breeding, disease monitoring, and sustainable livestock management has been greatly increased by recent developments in high-throughput sequencing, bioinformatics, and multi-omics integration. This review highlights the revolutionary potential of metagenomics in livestock production systems by examining its methodological advancements, historical background, and diverse applications.