Proteomics, the large-scale study of proteins and their functions, is an essential tool in biological research, particularly in livestock production and aquaculture. This review explores the significance of proteomic techniques and technologies in enhancing agricultural practices. Key methods, including mass spectrometry, two-dimensional gel electrophoresis, and protein microarrays, enable researchers to analyze protein complexity in biological systems. In livestock production, proteomics improves animal health, growth, reproduction, and disease resistance, contributing to more efficient and sustainable practices. In aquaculture, it optimizes fish health, breeding strategies, and feed efficiency, promoting sustainable farming. Despite its potential, proteomics faces challenges, such as complexity, the need for standardized methods, and difficulties in data interpretation. However, emerging advances—including multi-omics integration, real-time monitoring, and improved understanding of protein functions under varying environmental conditions—offer promising solutions. In conclusion, proteomics is poised to transform livestock production and aquaculture, addressing key challenges in food security and sustainable agriculture.