Genome-wide overwintering gene expression studies in bees are of critical importance to understand their survival, life cycles, and fitness. In this study, we use RNA sequencing to characterize the genes and gene functions associated with overwintering adult females compared with active season females for the small carpenter bee, Ceratina calcarata. We found extensive changes in gene expression associated with overwintering, including an underrepresentation of genes related to muscle fibers and an overrepresentation of genes related to lipid metabolic processes. These data suggest inactive, overwintering bees invest heavily in the production of proteins related to fat storage and divest transcriptional activity away from cellular and muscular structural processes. This study provides the first characterization of overwintering gene expression as important baseline data of a major life history event relevant to survival and health for a wild bee pollinator.