Being at the food chain apex, polar bears (Ursus maritimus) are highly contaminated with persistent organic pollutants (POPs). Females transfer POPs to their offspring through gestation and lactation; therefore, young cubs present higher POPs concentrations than their mothers. Recent studies suggest that POPs affect the lipid metabolism in female polar bears; however, the mechanisms and impact on their offspring remain unknown. Here, we hypothesized that exposure to POPs differentially alters genome-wide gene transcription in the adipose tissue from mother polar bears and their cubs, highlighting molecular differences in response between adults and young. Adipose tissue biopsies were collected from 13 adult female polar bears and their twin cubs in Svalbard, Norway, in April 2011, 2012, and 2013. Total RNA extracted from biopsies was subjected to next-generation RNA sequencing. Plasma concentrations of summed polychlorinated biphenyls, organochlorine pesticides, and polybrominated diphenyl ethers in mothers ranged from 897 to 13620 ng/g wet weight and were associated with altered adipose tissue gene expression in both mothers and cubs. In mothers, 2502 and 2586 genes in total were positively and negatively, respectively, correlated to POP exposure, whereas in cubs, 2585 positively and 1690 negatively genes. Between mothers and cubs, 743 positively and negatively genes overlapped between mothers and cubs suggesting partially shared molecular responses to ΣPOPs. ΣPOP-associated genes were involved in numerous metabolic pathways in mothers and cubs, indicating that POP exposure alters the energy metabolism, which, in turn, may be linked to metabolic dysfunction.