In 1863 Father Philip Shannahan was appointed as the first resident pastor. In the years following, the parish was served by Father Patrick McGinnis, Father Philip Laurent from Saint Mathias in Muscatine, and Father John J. McCabe.
During the pastorate of Father Quigley in 1867 plans were made for a new brick church. The church was completed in 1868 under the pastorate of Father P. A. McCabe, who served until 1872. A new steeple was added in 1900-1901.
Over the years the pastors of Saint Mary's, Wilton, reached out to serve Catholics in many surrounding communities including West Liberty, Durant, Tipton, Ardon (once known as "Seventy-Six"), "Nichols Station", "Irish Valley" and "The Settlement."
The church building was remodeled several times over the years. The church interior was remodeled in 1929-1930 and again in 1950. In 1950, the walls of the building were bound together with steel rods and a new tile ceiling was installed. The sanctuary was remodeled with a beautiful oak crucifix and altar. A terrazzo floor, oak pews and altar railings completed the interior.
In 1953 the rectory was gutted by fire. A new brick structure was built on the old foundation.
A new brick parish hall was completed in 1961. This building served as a religious education center as well as a meeting place for parish organizations. In 1966, a lowered tile ceiling was placed in the church. Reflecting current liturgical thought, a new altar was built from the existing communion railing and was made to face the congregation. The church was redecorated, including the laying of a red carpet. Changes and improvements to the church continued during the 1970's. A reconciliation room was constructed for the sacrament of penance and new church doors were donated. In 1981, a new choir loft was built and an addition added a sacristy, office, and five classrooms.
The brick church was razed in 1987 due to structural problems that had grown too expensive to fix. The parish hall began to be used for worship.