Adipose tissue is the primary fuel storage for vertebrates and is an important component of energy budgets during periods of peak energetic demands. Investigating the composition of adipose tissue can provide information about energetics, migration, reproduction and other life-history traits. Until now, most field methods for sampling adipose tissue of small-bodied vertebrates have been destructive. Therefore, investigations of adipose tissue in small-bodied vertebrates have been limited in their broadscale application. We developed a field-ready micro-adipose biopsy method for sampling adipose tissue of small-bodied vertebrates, by adopting fine-needle adipose aspiration. We applied the method to silver-haired bats (Lasionycteris noctivagans) and then quantified the resulting fatty acid signatures of a summer group and an autumn group to demonstrate one possible application of the method. We successfully obtained interpretable fatty acid signatures from 74·5% of micro-adipose biopsy attempts, with success positively correlated with body mass index. Summer and autumn groups of bats had different fatty acid signatures likely representing varied available dietary compositions at resident sites (the habitat where adipose deposits are accumulated prior to migration). The fatty acid profile of autumn silver-haired bats was largely characterized by 16:0, 18:1 and 14:0, and the summer group was characterized by 16:0, 16:1 and 18:0. Our results suggest that fatty acid signatures have the potential to characterize the origins of migrating individuals, or the number of unique subpopulations being supported by a migration route. This field-ready fine-needle adipose aspiration method can be used on small-bodied mammals and modified for application to other small-bodied vertebrates. This non-destructive approach to sampling adipose tissue has great value because it allows for robust sample sizes, longitudinal studies of the same individuals across space and time, and sampling of rare, threatened and endangered species.