I managed to solve the issue by debugging the agent. I found out that despite the None _company.com:1234/our_gitlab/our_repo.git line I found out that it was actually trying to clone from the url None _company.com:1234/our_gitlab/our_repo.git . The agent host machine therefore didn't try to use the git user, but the session user ec2-user resulting in a permission denied error.

I solved it by adding an entry in the agent's ~/.ssh/config to force the use of user git every time it tries to connect to the host where my gitlab instance is served:

Host ourtools.ourcompany.com
    User git
    Hostname ourtools.ourcompany.com
    IdentityFile ~/.ssh/id_ourcompany