Obesity in childhood is associated with adulthood obesity, type 2 diabetes (T2D), and future metabolic complications. The gut microbiome is a modifier of host metabolic function with altered bacterial composition associated with disease risk. Few studies have investigated the relationships between metabolic disease, inflammation and the gut microbiota in youth where these connections likely originate. Here we characterized the gut microbiome of a cohort of 56 non-diabetic adolescents with obesity using fecal DNA sequencing with absolute bacterial quantitation together with immune and metabolic profiling. We observed multi-log order variation in absolute bacterial biomass dependent on host environment and associated with bacterial taxonomic composition based on a nested case-control comparison. Participants with higher biomass displayed a healthier phenotype with higher gut microbiome diversity, lower abundance of taxa associated with inflammation and pathogenicity such as Escherichia Coli, and lower levels of neutrophil activities. Further association analysis revealed sex-dependent variation, with higher levels of insulin resistance, fasting triglycerides, and markers of neutrophil activities in male adolescents with lower bacterial biomass. Together these results suggest that intestinal bacterial biomass and composition are associated with metabolic and inflammatory dysregulation evident before T2D diagnosis and identify sex differences in microbiome-associated metabolic dysfunction in adolescents with obesity.