Cardiac surgery with cardiopulmonary bypass may be necessary in patients with pre-existing, continuous-flow, left ventricular assist devices. Heart transplantation or exchange of a malfunctioning left ventricular assist device are the most common scenarios. However, reoperation may also be needed for acquired valvular disease or device malposition. In these cases, operative strategies that enable safe conduct of cardiopulmonary bypass and, if needed, cardioplegic arrest while the left ventricular assist device remains in situ, are essential. Such strategies would avoid unnecessary replacement of working components of the left ventricular assist device and, importantly, avoid damage to them during the period of cardiopulmonary bypass. Adequate anticoagulation, avoidance of regurgitant flow into the device, prevention of blood stagnation in the hardware and careful deairing after periods of pump stoppage are key principles. We present a stepwise algorithm for the management of the HeartMate II device during such cases.