The commercial importance of cotton as the primary crop producing a renewable source of fiber for the textile industry and cottonseed oil for the food industry is the main driving force behind the study of these species. Metabolomics techniques have been broadly used to improve our understanding of fundamental aspects of cotton fiber development. Biological processes of cotton fiber development, including fiber cell elongation and secondary cell wall biosynthesis, have been subjects of extensive metabolomics analyses. Metabolite profiling studies have been used to select cotton cultivars with healthier ratios of the essential fatty acids extracted from cottonseeds for oil, providing a powerful resource to guide breeding programs. These studies have significantly expanded our knowledge and continue to do so concerning many aspects of the cotton fiber and cottonseed oil phenotypes. Furthermore, an increased understanding of the genetics of cotton, large-scale phenotyping approaches, the recently available drafts of the cotton genome sequence, as well as advances in the next-generation sequencing technologies, have generated many novel research concepts that are also placing metabolomic analysis as an essential component of cotton research.