Covenant's Aeolian-Skinner-Holtkamp organ is known as one of the landmark pipe organs in the Midwest. Built by the E. M. Skinner Company in 1930, it was rebuilt and enlarged by the Aeolian-Skinner Company in 1958. In December, 1996, a new console crafted by the Holtkamp Organ Company was installed.

Besides being a beautiful piece of furniture, the console includes the most current solid-state technology being employed in the organ industry. There are 256 "levels of memory," meaning that every combination button on the organ can be set 256 times. There is also a digital record/playback system, and the console is moveable to the center of the chancel for recitals and concerts.

Five new stops were added to the organ, including two new reeds (members of the trumpet family) and a new Cornet ("cor-nay") which is a special solo color used especially for leading hymn tunes. Two new 32' stops were also added. These are the lowest pitches in the organ and they greatly improve the sense of undergirding and support for congregational singing. These low pitches are produced by a large electronic speaker placed in the organ chamber. This work brings the organ thoroughly up-to-date in terms of technology and fills in critical holes in the tonal scheme.