Problem was that my RSA key had a password. From my host machine it wasn’t necessary to input the password as the ssh-agent was acting as a frontend for my SSH libs and it kept the password encrypted in memory.
This was not the case of the virtual machine, practically empty and only with the .ssh folder (with correct rights and for the correct user). I fixed this and automatized the solution by adding a RUN command in my Dockerfile to change the password to an empty string, which allows to pull from git when building the image. I haven’t found any parameter under /etc/ssh that being changed allow me to connect without entering the password, so I must assume that the password step is mandatory in the RSA protocol to ensure confidentiality with the user, even if cyphering with the user’s public key is sufficient to ensure it.
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solved Authenticating a virtual machine against a Gerrit git server