Chelation therapy is recognized as a safe and effective treatment option in patients with beta-thalassemia with iron overload. We report an 18-year-old male with acute abdomen and gastrointestinal bleeding with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection secondary to gastric perforation due to chelation therapy. This patient had a prolonged intensive care stay with complications of SARS-CoV-2 and a small bowel obstruction post-surgery that resolved after conservative management. Given the acute presentation, chelation therapy use and concomitant SARS-CoV-2 infection, clinicians should keep an open mind on the differential diagnosis of acute abdomen in patients with beta-thalassemia.