A local legend credits monks from the monasteries of Nydala and Varnhems kloster with building the original church. For a long time, however, its actual age remained unknown. A dendrochronological study of the roof timbers carried out in spring 2005 finally established that the oldest parts of the building date from sometime between 1192 and 1255, placing its origins firmly in the medieval period.
The church has been altered over the centuries. In 1781 it was extended eastward, creating the present chancel and removing an old vaulted arch that had separated chancel from nave. A new sacristy was built in 1785, replacing an earlier wooden one from 1637, and the porch at the west gable dates from 1892–1895.
The timber bell tower was erected in 1693 and originally painted red; it was later whitewashed during the nineteenth century before being tarred again in 2006 for better weather protection. Three bells hang within it: the largest was recast in 1738, the smallest bought in Jönköping in 1710, and the newest cast in 1907. Until 1992 the bells were rung by hand.
Among the church's furnishings, the Romanesque stone font dates from the twelfth century, and a communion vessel from the 1200s is thought to have been made in Germany. The pulpit, carved in 1646, originally stood in Villstads kyrka before being bought for Våthult in 1749 and installed in 1751.
The present organ, built in 1987 by Ingvar Johansson of Västbo Orgelbyggeri, reuses the façade of an earlier 1912 instrument by Johannes Magnusson of Gothenburg, itself a replacement for an 1889 organ donated by a local factory owner born in Våthult.