You are returning the result of the last Logger.debug expression which is :ok

If you really wanted the “end of confirm_email” logging you need to return the result after.

  def confirm_email!(user = %User{email_confirmed: false}) do
    confirm = User.changeset_confirm_email(user, true)
    result = case Repo.update(confirm) do
      # Updated with success
      {:ok, updated_user} ->
        Logger.debug("update success")
        {:ok, updated_user}
      {:error, _, reason, _} ->
        Logger.debug("update error")
        Logger.error(reason)
        {:error, reason}
    end
    Logger.debug("end of confirm_email")
    result
  end

I deleted my response by mistake.

You were right, the root problem was the router. I was calling
get("/confirm_email/:token", UserController, :confirm_email) # for json api

and not:

get("/confirm_email/:token", SignupController, :confirm_email)

SignupController:

  def confirm_email(conn, %{"token" => token}) do
    Logger.debug("confirm_email token: #{token}")
    case Accounts.confirm_email!(token) do
      {:ok, updated_user} ->
        conn
        |> Guardian.Plug.sign_in(updated_user)
        |> put_flash(:info, gettext("Welcome %{user_name}!", user_name: updated_user.name))
        |> redirect(to: Routes.page_path(conn, :index))
      {:error, reason} ->
        Logger.debug("error reason: #{reason}")
        json(put_status(conn, 404), %{error: "invalid_token"})
    end
  end

Works fine. Thanks for the help. Guilty of programming while tired.
Leaving this here so others might benefit.

The last statement in your function is Logger.debug call, so it’s return will be your return value