Various organs are available at the HfMDK: In addition to the two large hall organs, there are six organs in overhead rooms and an Italian baroque organ.

There are also collaborations with various Frankfurt parishes, so that a wide variety of instruments are available for lessons and examinations. These include the Schuke organ in the Johanniskirche in Frankfurt-Bornheim and the Albiez organ in the Mutter vom Guten Rat church in Frankfurt-Niederrad.

Furthermore, regular projects take the students to the Walcker organ in the Lutherkirche in Wiesbaden and the Klais organ in the Christuskirche in Karlsruhe.