Nutritional management in inflammatory bowel diseases (IBD) is transitioning from a calorie-centric approach to a functional paradigm that incorporates body composition, metabolic health, and inflammatory burden. Malnutrition, which may manifest as sarcopenia, myosteatosis, or sarcopenic obesity, affects a significant proportion of patients from the time of diagnosis and has prognostic implications for treatment response, surgical outcomes, and quality of life that go beyond those associated with Body Mass Index (BMI) alone. This narrative review explores the evolving role of nutrition as both a disease modifier and a therapeutic adjunct in IBD, emphasizing mechanistic evidence that links ultra-processed foods and dietary additives to intestinal barrier disruption, dysbiosis, and persistent low-grade inflammation. We propose a phase-specific framework that positions nutritional assessment and dietary intervention as essential components of routine IBD care. During active disease, targeted exclusion diets can function as therapeutic adjuncts or, in selected cases, as primary interventions. During remission, adherence to anti-inflammatory dietary patterns, particularly the Mediterranean diet, promotes microbiota diversity, mucosal integrity, and long-term metabolic resilience. Nutritional interventions should be coordinated with pharmacological therapy to capitalize on the therapeutic window created by inflammatory suppression, thereby overcoming anabolic resistance and optimizing muscle protein synthesis. Standardized screening tools that integrate the Global Leadership Initiative on Malnutrition (GLIM) criteria with body composition analysis facilitate early identification of nutritional phenotypes and guide personalized interventions. By outlining current evidence and identifying remaining knowledge gaps, this review offers a strategic framework for precision nutritional care in IBD, positioning diet as a cornerstone of holistic disease management alongside advanced therapies.