We determined the fatty acid signatures in milk, serum, and blubber samples collected from young free-ranging Steller sea lions (Eumetopias jubatus) and investigated the partitioning of fatty acids among these matrices. We assessed the relationship of fatty acids in each matrix with region, age, season, sex, and body condition to gain information needed to determine the most appropriate type of samples to collect and analyze to address future research questions. The variability of fatty acid composition was almost entirely explained by sample type, highlighting the importance of selecting a matrix consistent with the study objectives. Regional differences in fatty acid composition were found in all sample types and these differences varied among matrices. The proportion of fatty acids in milk and serum were influenced by season of capture whereas blubber samples were more affected by age of the pup. The influence of season on the fatty acid signatures in milk and serum highlights the use of these samples over blubber in studies investigating seasonal changes in diet. Further, our findings suggest that the use of milk samples collected from the stomachs of pups may be a viable alternative to directly collecting milk from adult females.