The earliest known church on this site was a small medieval timber building, destroyed by a forest fire in 1652 along with the neighbouring rectory. A replacement timber church was built, likely resembling its predecessor, but by the eighteenth century the parish had grown considerably and the wooden church could no longer accommodate the congregation; worshippers reportedly had to stand in double rows during services. Plans to enlarge the old building were abandoned in 1722, partly because the structure was thought too unstable and partly due to the hardship following the wars of Karl XII.
In 1752 the parish decided to build an entirely new church. Timber was initially intended, but sufficient wood proved hard to source, and growing concerns about fire risk favoured stone construction instead. The new church was built in grey stone between 1753 and 1757, while the old timber church continued to serve the congregation during construction; it was later demolished, though its bell tower was left standing. Sources differ on the exact consecration date, with one account citing 1757 and another 1775 under Bishop Magnus Beronius of Kalmar.
The building was later enlarged in stages. A tower was added in 1830, designed by C.G. Blom Carlsson and built under master builder Hallström, topped with a rendered brick lantern. Continued population growth, especially in the Nybro area, required further expansion, and in 1885 the present chancel, apse and sacristy were added, making Madesjö one of the largest rural churches in the former Diocese of Kalmar.
Inside, the church holds a red limestone font dated to 1655, considerably older than the current building. The rococo pulpit, carved in 1773 by Jonas Berggren, and an older altarpiece from the same year and sculptor, are notable survivals from the church's early furnishing. A large copy of Bertel Thorvaldsen's Christ figure from Our Lady's Church in Copenhagen once served as an altar image. A modern triumphal crucifix, created in 1988 by Sven-Bertil Svensson of Mörbylånga, hangs among symbols of the four evangelists in the transepts.
Among the church's most striking features are the three chancel windows created in 1930 by the Nybro artist Gunnar Theander, each composed of around a thousand pieces of coloured glass. The central window was completed by Sven-Bertil Svensson following Theander's death. The church has also had a succession of organs since 1707, the current gallery organ dating from 1991 and built by Åkerman & Lund, alongside a smaller mechanical choir organ from 1973.