The first worship service of Atonement Lutheran Church was held on September 10, 1961 in the Cafetorium of Lackland City Elementary School with 150 persons present. The congregation was officially organized on December 17, 1961 with a charter membership of 145 baptized members representing 40 families. The dedication of the church building took place on May 27, 1962. Membership by this time had risen to 206. A basement below the sanctuary was dedicated on August 21, 1966. Membership in the late 1960s stood at 583 baptized members representing 139 families. Sunday school attendance was as high as 200 children. In the early 1980's Atonement established a mission church that continues to be active today.

In 2000, the congregation set a goal to renovate Atonement to make the church more inviting to visitors and members. Improvements included the installation of a lawn sprinkler system, drainage work around the facility to eliminate erosion, installation of a modem playground, remodeling of the restrooms to make them ADA compliant, and renovations to the interior to include textured wall covering, improved lighting, painting, new doors and hardware, flooring, and pew cushions. This was the first major renovation for Atonement since the construction of the basement in 1966. Just in time for Atonement's 40th anniversary celebration to the Glory of Jesus Christ!