On March 20, 1988, the Voter's Assembly resolved to become two separate congregations, and an Implementation Committee was established to work out the details of the separation. Celebration Sunday was held onJuly 31, 1988 with final joint worship services at Calvary Lutheran and Messiah Lutheran. That same year saw Pastor Goldhammer resign effective August 1, the church office re-established at 28th and Franklin, and an Anniverasry Committee appointed to recognize and plan for the church's 60th anniversary.

Reverend Roger B. Henning was installed on January 8, 1989. The bookstore was sold and Calvary Foundation began acquiring surrounding properties for future expansion, including a parking lot. On May 17, the congregation celebrated 60 years of blessings.