<p>Pediatric inflammatory bowel disease (IBD) is a chronic and relapsing disorder with rising global incidence. Gut microbiota dysbiosis and metabolic alterations have been implicated in disease pathogenesis, yet their precise roles in pediatric IBD remain incompletely understood. This review synthesizes current evidence on the interplay between the gut microbiota and metabolomics in pediatric IBD, highlighting their contributions to disease onset, progression, and therapeutic response. We examine changes in microbial composition, alterations in short-chain fatty acid, bile acid, and amino acid metabolism, and their effects on intestinal immunity and barrier function. In addition, we discuss microbiota-based therapies, such as probiotics, prebiotics, and fecal microbiota transplantation, along with the potential of metabolomic profiles for diagnostic and prognostic use. Finally, we emphasize integrating multi-omics approaches to uncover novel therapeutic targets and advance precision medicine strategies in pediatric IBD. A deeper understanding of microbiota–metabolite interactions may pave the way for personalized interventions to improve clinical outcomes in pediatric patients with IBD.</p>