The invention provides a method, system and tuning devices for reed and flue pipes for automatically tuning or checking the tuning of a pipe organ. The invention enables the tuning of the reed pipes to the same pitch as flue pipes if the fluctuation of temperature and humidity has caused a change in the pitch of the flue pipes, and to restore the tuning of the reed pipes in case of random loss of tuning. The invention allows to reduce the tuning time and to tune the pipes that require more frequent tuning (i.e. the reed pipes) unobtrusively to the organist and listeners during the playing of the organ. It is possible to employ the method of the invention on all pipes of an organ or only on a selection of them.