Iron deficiency and anemia are common in patients with inflammatory bowel disease (IBD), requiring effective and well-tolerated iron replacement strategies. While oral iron is widely used, growing evidence suggests it can disrupt the gut microbiota by reducing beneficial commensal bacteria and promoting pro-inflammatory shifts in the intestinal environment. These changes may exacerbate mucosal inflammation and contribute to gastrointestinal side effects, often resulting in poor adherence. Intravenous iron, by bypassing the gastrointestinal tract, appears to have a less disruptive effect on the microbiota and may more reliably restore iron stores, particularly in patients with active disease or intolerance to oral formulations. Current expert recommendations support intravenous iron as the first-line option in such cases, though oral iron remains a practical choice for selected patients with mild anemia and inactive disease. Emerging research also raises concerns about the safety of oral iron in vulnerable populations, as it may promote dysbiosis and expansion of potentially pathogenic bacteria. In response, adjunctive strategies are being explored to support the microbiota and improve the tolerability and efficacy of oral iron. Incorporating microbiota-related considerations into treatment decisions may enhance outcomes and reduce side effects. Future clinical guidelines should reflect the evolving understanding of the gut microbiome's role in iron metabolism and inflammation, promoting more personalized, microbiota-conscious approaches to iron therapy in IBD.