Nosocomial infections and thrombosis are frequent complications during extracorporeal membrane oxygenation (ECMO). Preventative measures and close monitoring for early recognition of these complications are imperative in patients supported with ECMO. We report the case of a 41 year old female on veno-venous ECMO awaiting surgical thrombectomy for chronic thromboembolic pulmonary hypertension that developed profound bacteremia leading to gross purulence and thrombosis of the membrane oxygenator. Recannulation in addition to targeted antibiotics, frequent cultures, imaging, and surgery were diagnostic and therapeutic interventions that led to ultimate resolution.