The organ occupies the north transept of this cruciform building. Of note is the suspended Positive division, which is placed between the gallery floor and the detached console below. The organ has mechanical key action and electric stop action. A number of pipes were retained from the Abbey's previous instrument.

Recent renovation of the Abbey Church was directed by Frank Kacmarcik, Liturgical Consultant, and Lee Tollefson of Rafferty Rafferty Tollefson Architects of St. Paul. Acoustician Robert Mahoney has provided valuable advice on preserving the fine acoustics of this space, which has a reverberation time of more than four seconds at mid-range frequencies.

Delores Bruch served the Abbey as Organ Consultant. Fr. Sean Duggan is the Abbey Organist.