This is perhaps quite simple, but I haven\'t found anything useful when googling. So here it goes :)
I use Emacs in daemon mode (emacs --daemon) and it\
To expand on phils' answer:
On Emacs 26.1 I had to run the keyboard translations in the context of the new frame, like so:
(defun make-keyboard-translations ()
(keyboard-translate ?\C-j ?\C-c))
(defun setup-frame-keyboard (frame)
(with-selected-frame frame
(make-keyboard-translations)))
(make-keyboard-translations)
(add-hook 'after-make-frame-functions #'setup-frame-keyboard)