Celiac Disease (CD), also known as non-Tropical sprue, and Celiac sprue is an immune-mediated disorder, triggered by gluten containing grains in genetically susceptible people. The disease may be diagnosed at any age and can affect many organ systems. Its diagnosis and management can often be challenging. A high index of suspicion is required to diagnose this disease at an early stage in patients presenting with atypical symptomatology and delayed onset. Although serological tests are widely used, duodenal biopsy remains the gold standard for diagnosis of CD. Even though CD affects various body systems, Microscopic Colitis (MC) and refractory sprue are among the main gastrointestinal complications of CD, which are resistant to Gluten-Free Diet (GFD). A thorough and appropriate evaluation is mandatory for an early and accurate diagnosis of these complications. Herein, we report a case of a young female with CD in early phase in concordance with MC and splenomegaly.