The answer is simple but also not completely obvious to someone new to the platform. So you can inject new command line args that hydra will recognize. This is what the Hydra section of args is for. However, if you enable _allow_omegaconf_edit_: True , I think ClearML will “inject” the OmegaConf saved under the configuration object of the prior run, overwriting the overrides. I’ll experiment with this behavior a bit more to be sure.