The church now known as the Lyons Evangelical Free Church began as a mission work by the members of the Lyons Union Sunday School Association in the 1890s. A.J. Lundberg, member of Riverside Methodist Church, became the first teacher and later became a superintendent. Land on Joliet Avenue in Lyons was donated for a Sunday School building and a building was constructed where Lyons' Fire Station now stands. A Mr. Evans was first superintendent of the Sunday School, which later became known as Bethel Chapel.
Between 1921-1931, the Sunday School met regularly and a worship service was held until 1937 when Bethel Chapel lost its building. During the 1930s and 40s others were superintendent, including Gil Larimer. Prominent among these leaders was John R. Robinson, who served the Sunday School from 1921 until his death in 1961.
Bethel Chapel's Sunday School met regularly at the Lyons Sokol hall between 1937 and 1957, when a weekly worship service was begun by Trinity Evangelical Divinity School student R. Ivan York. In 1959, the group incorporated as the Lyons Evangelical Free Church with 20 charter members. Pastor York was succeeded by Edson A. Fast.
The congregation keenly felt the need for their own building. The Sokol hall was often used for parties on Saturday nights and the group frequently had clean up and air out the building from the evening's activities. In 1960 the Sokol hall was sold and the group began worship services in the Lyons Village hall. York and Fast urged the congregation to purchase a church building and adjacent parsonage up for sale by St. John's Evangelical and Reformed Church, a building which had originally been built by St. Mary's Roman Catholic congregation in 1875. The purchase was completed and on December 3, 1961 the first services were held in the building, which has housed the Lyons Evangelical Free Church to the present day. Also in 1961 an evening service was instituted. In May, 1962, Pastor Fast resigned to go to other work and Dr. Jerome Ficek, Trinity Evangelical Divinity School professor, became interim pastor. The church held its first Vacation Bible School in 1962 and Rev. Carroll Swenson became pastor in September of 1962.
A youth work was begun in 1960 and in the same year the Women's Missionary Society received its national charter. In 1963 the church held its first missions conference, involving Wil Andersons, Jack Loshbough, Don Carlson and Andrew Furuyama.
The group developed and adopted its first constitution in 1964. In 1966, Trinity Evangelical Divinity School student Ivan York, became pastor and Carroll Anderson served from 1969 until 1979. AWANA youth clubs were started in 1971 and the building was renovated with a new heating system and aluminum siding in 1972. In 1975 the building was designated a Lyons Landmark by the village. Another interim pastor, Philip Cherico, served in 1979 and Allan Peterson became pastor in 1980.