Background Internalizing disorders and cardiometabolic disease are common conditions that frequently co-occur in later life and may be attributed to shared genetic influences. While phenotypic effects of polygenic liability of adult disorders may emerge early in life, studies have not investigated this in the context of multimorbidity. This study set out to investigate early manifestations of polygenic liability to adult internalizing-cardiometabolic multimorbidity (ICM-MM) in a UK population birth cohort. Methods We used data from 5,821 individuals in the Avon Longitudinal Study of Parents and Children (ALSPAC). We modelled trajectories of 12 mental and cardiometabolic health outcomes using mixed effects models, and investigated effects of adult ICM-MM polygenic liability on these trajectories. We also investigated associations of adult ICM-MM polygenic liability with circulating inflammatory proteins (Olink Target 96 Inflammation panel) at ages 9 and 24. Results Adult ICM-MM polygenic liability is associated with cardiometabolic traits and inflammation, and with changes in depressive symptoms and cardiometabolic traits over time in childhood through to early adulthood. A notable early life biological footprint is inflammation. We found that higher ICM-MM polygenic liability is consistently associated with higher interleukin-6 (IL6), tumor necrosis family superfamily member 14 (TNFSF14) and hepatocyte growth factor (HGF) levels in both childhood and early adulthood. Conclusions Adult ICM-MM polygenic liability manifests early in life through changes in mental and cardiometabolic health and blood biomarkers, especially in increases of circulating inflammatory proteins related to obesity, immune cell chemotaxis and migration that may contribute to disease pathogenesis by seeding inflammation in relevant tissues.