The story of a church at Lönneberga stretches back to the Middle Ages. Parish records beginning in 1597 mention a donation in 1341 linked to an early wooden chapel, which was later replaced by another building. A surviving triumphal crucifix from the mid-1300s also points to a medieval church on the site. That first structure was apparently demolished towards the end of the 1500s and replaced with a new timber church, which was then destroyed by fire during Danish raids in July 1612, in the course of the Kalmar War. A further church, built of stone and timber, rose four years later and served the parish until the 1870s.
The current building dates from 1870–1872, designed by the architect Johan Fredrik Åbom. Unusually, the church is oriented the 'wrong' way round, with the tower to the east and the chancel and altar to the west. The tower is topped by an open lantern. A major renovation in 1924–1925, overseen by architect Otar Hökerberg, added a semicircular sacristy beside the chancel on the western gable end, replacing an earlier sacristy that had occupied a rounded extension on the north side of the nave. In 2004 clear plexiglass panels were fitted into the lantern's openings to help prevent damp damage.
Among the church's furnishings, the oldest is the triumphal crucifix dating from the 1300s, saved from the earliest church on the site. From the second church come surviving paintings, a candle bracket and an oak bridal chair. The wooden font was made in 1933.
The main organ was built in 1874 by Erik Nordström of Flisby, originally with ten stops, and was rebuilt in 1925 by E. A. Setterquist & Son; it was renovated and its disposition altered in 1957, and later work in 1994–1995 aimed to restore it as closely as possible to its original form. A separate, mechanically operated chancel organ by Nils-Olof Berg of Nye, decorated by Lennart Lindell, was installed at the north wall of the chancel and inaugurated in September 1978.