Yes, of course it can be done. Not that easy with “regular” mix ecto.migrate, but there is several ways to do so:

1. Create additional environment for migrations (for example MIX_ENV=migrate) and then create config/migrate.exs where you configure options for your migrations user (additionally you can add preferred_cli_env: ["ecto.migrate": :migrate] to not need to remember to set proper environment each time you run migrations).
2. Create custom migration task where you will do:

   {:ok, pid} = MyApp.Repo.start_link(name: :migrations, user: "foo", password: "bar")
   Ecto.Migrator.run(MyApp.Repo, :up, all: true, dynamic_repo: :migrations)
   :ok = MyApp.Repo.stop(pid)
   

3. Use environment variable with config/runtime.exs or Repo.init/2 callback (often DATABASE_URL is used) and then provide different user each time you run application in different scope.

What approach you will use depends fully on your needs and use cases.