During the mid and late 1800s, Poygan looked after the mission parishes in Omro and Winneconne until those congregations built their own churches. St. Thomas prospered at the end of the 19th and the beginning of the 20th centuries when the church was remodeled and a barn and new rectory built. The parish was closed in 1969 and placed under the jurisdiction of St. Mary in Winneconne. As a non-functioning church, the Winneconne pastor or his appointee could celebrate only five Masses per year there. Special permission had to be given for other liturgies or celebrations.
Various groups continue to look after it.
The St. Thomas Christian Mothers clean the building and launder the altar linens. The St. Thomas Cemetery Association administers the cemetery. The Friends were organized in August of 1998 under the leadership of Wicinsky and her husband, Mike. Meetings are held the third Sunday of each month. Membership numbers about 75.