Built from 1885 – 1887 under the guidance of Father John Marie Garnier, the parishioners built this church – the largest church in Lincoln County at that time – a little over 3,000 sq. ft. The church is built of adobes made on site and vigas hauled in from the Capitan Mountains.
In 1973 the remaining resident parishioners recommended the church be sold to the State of New Mexico in order to protect it from further decay. The building was restored by the State and was opened to the public in 1984.
In 1986, the windows in the church were worked on but, instead of restoring the original windows, a second frame was put over them. Since then, the original frames deteriorated to such an extent they required immediate attention. Restoration work was completed in July of 2015 on the eleven exterior windows.
The San Juan Mission is currently in need of various repairs ranging from plaster, stucco, paint and wood restoration work.