The present invention extends to methods, systems, and computer program products for reconfiguring an acceleration component among interconnected acceleration components. Aspects of the invention facilitate reconfiguring an acceleration component among interconnected acceleration components using a higher-level software service. A manager or controller isolates an acceleration component by sending a message to one or more neighbor acceleration components instructing the one or more neighbor acceleration components to stop accepting communication from the acceleration component. The manager or controller can then shut down an application layer at the acceleration component for at least partial reconfiguration and closes input/output (I/O) portions. After reconfiguration completes, communication between the acceleration component and the one or more neighbor acceleration components can resume.