To update to the latest version of Portainer Server, use the following commands to stop then remove the old version. Your other applications/containers will not be removed.

docker stop portainer
docker rm portainer

Now that you have stopped and removed the old version of Portainer, you must ensure that you have the latest version of the image locally. You can do this with a docker pull command:

docker pull portainer/portainer-ce:latest

Finally, deploy the updated version of Portainer:

docker run -d -p 8000:8000 -p 9443:9443 --name=portainer --restart=always -v /var/run/docker.sock:/var/run/docker.sock -v portainer_data:/data portainer/portainer-ce:latest