 <p>When stopping the server you should try to use the stopServer(node/manager/etc).sh </p> <p>Now as it was mentioned before in the comments, if you are seeing that error it means that there are still some other WebSphere process running. Check the process by going into the Task Manager -> Processes (Check the Box for "Show processes for all users").</p> <p>Usually the WAS process are named java and WASService.exe. The java process for dmgr is usually 200,000K or more, Node Agent and Servers might be smaller depending on your env. The WASService.exe is much smaller than the java.exe one. Now you could kill these processes and that should help. In addition to that you can go to the Services section of the task manager and you can review the ones known as IBMWASXXServices and these can also be stopped (I think someone else suggested this as well). </p> <p>Finally if you keep struggling with this issue, it might be good to open a PMR with IBM and you will be helped to solve the issue. </p>