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There is a very good question on SSH to Elastic Beanstalk instance, but one thing I noticed is that, through this method, it is only possible to add one SSH key.

How can I add multiple SSH keys to an instance? Is there a way to automatically add multiple keys to new instances?

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The answer is NO. Elastic Beanstalk only supports a single key pair. But you can manually add ssh keys to authorized_keys file, but the keys which are added will not be known or access by Elastic Beanstalk tools.

You can create a file named .ebextensions/authorized_key.config is also a way to do it.

files:

  /home/ec2-user/.ssh/authorized_keys:

    mode: "000400"

    owner: ec2-user

    group: ec2-user

    content: |

      ssh-rsa AAAB3N...QcGskx key_name

      ssh-rsa BBRdt5...LguTtp another_key

The name of file authorized_keys.config is arbitrary.

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