Impressive instruments in an outstanding acoustical environment give Luther organ students a complete musical education. 5 mechanical key-action pipe organs offer students ample practice facilities. The Rost Memorial Organ, located in the Center for Faith and Life, is a 62-rank, mechanical key-action organ with 42 independent registers. Played almost daily by student organists and the college organist, the organ is an integral part of daily chapel and weekly Sunday worship. Organ students also have the opportunity to work with local churches, directing choirs and performing at worship services. Four organs are available for student use in Jenson Hall of Music, including the Sundt Organ, a 37-rank, 25-stop instrument. At the core of the organ program are applied lessons. Taught by college organist Gregory Peterson, these lessons are open to all students regardless of major.

Students receive academic credit for private lessons, although the cost of these lessons is not included in the comprehensive fee.