Omics technologies (mainly, proteomics, transcriptomics and metabolomics) have been highly improved over the last years. The development of these tools has allowed important advances in the field of livestock science. In small ruminants (goats and sheep), omics approaches are a unique tool to increase the understanding of the different physiological and biological processes. Advanced and more sensitive proteomics techniques have provided crucial information about proteins present in colostrum from goats and sheep, especially those in low abundance. Differences in the colostrum proteome of both species suggest that the use of colostrum replacer or colostrum from other species may not ensure a correct passive immune transfer to the offspring. Furthermore, proteomics revealed that not only immunoglobulins are increased in blood of newborn lambs after colostrum feeding, but also several other immune proteins. Omics studies on small ruminants’ mammary gland are still scarce and mainly based on transcriptomic approaches. Mastitis is one of the most important diseases in dairy animals, and in this field, proteomics has been used to describe several inflammatory proteins in both mammary gland and milk. The adaptation of different breeds to harsh conditions (e.g., feed restriction) has been also studied using proteomics, although similar metabolomics-based studies did not show these differences between breeds. Additionally, transcriptomics and nuclear magnetic resonance-based metabolomics of blood, milk and urine in goats increased our understanding of how goats respond to heat and cold stress. Therefore, it seems that omics are powerful techniques to assess the effect of stressor factors. The general insight suggests that omics approaches are a very useful tool that contributes to explore different processes. The constant development of these techniques and the integration of several omics are recommended to clarify and accelerate the acquisition of knowledge. Finally, the versatility of omics approaches would contribute in the near future in the discovery of new biomarkers for fundamental processes, such as, welfare, health, metabolism, among others, in small ruminants.