Procellariiforms are unique among seabirds in storing dietary lipids in both adipose tissue and stomach oil. Thus, both lipid sources are potentially useful for trophic studies using fatty acid (FA) signatures. However, little is known about the relationship between FA signatures in stomach oil and adipose tissue of individuals or whether these signatures provide similar information about diet and physiology. We compared the FA composition of stomach oil and adipose tissue biopsies of individual northern fulmars (N = 101) breeding at three major colonies in Alaska. Fatty acid signatures differed significantly between the two lipid sources, reflecting differences in dietary time scales, metabolic processing, or both. However, these signatures exhibited a relatively consistent relationship between individuals, such that the two lipid sources provided a similar ability to distinguish foraging differences among individuals and colonies. Our results, including the exclusive presence of dietary wax esters in stomach oil but not adipose tissue, are consistent with the notion that stomach oil FA signatures represent lipids retained from prey consumed during recent foraging and reflect little metabolic processing, whereas adipose tissue FA signatures represent a longer-term integration of dietary intake. Our study illustrates the potential for elucidating short- versus longer-term diet information in Procellariiform birds using different lipid sources.