Chronic gastrointestinal (GI) complaints are often treated with proton pump inhibitors (PPIs), antibiotics, and other medications that offer temporary relief of acute symptoms. Although these drugs are prescribed to provide promising results, new research indicates the drug treatments often mask unresolved physiological problems and cause further complications. Complex GI cases require a comprehensive assessment and a multifaceted approach. This case reports on the development of PPI-induced hypochlorhydria secondary to a PPI prescription for unresolved gastritis in a patient with irritable bowel syndrome. The patient's gastritis and hypochlorhydria symptoms resolved with the implementation of a comprehensive functional nutrition approach that incorporated dietary guidelines, lifestyle recommendations, and customized nutritional supplementation and herbs.