Kapellendorf has one of the oldest known churches in Thuringia. A first church already existed on this site around 800. It shaped the name of the village: Kapellendorf. Founded as an aristocratic private church, the church was donated to the imperial monastery of Fulda in early times. In the 12th century, the parish church was a fief of the Burgraves of Kirchberg, who founded a Cistercian nunnery here in 1235. The nunnery existed for three centuries. It was dissolved in 1525 during the Reformation and the property and furnishings were confiscated. An inventory that still exists today provides information about this. The church was reduced in size and the nuns' choir was demolished in 1528/29. The south aisle was also removed in 1577 at the latest. Since then, the Kapellendorf church has once again served solely as a parish church. Numerous preserved funerary monuments inside bear witness to the great importance of the church as a place of burial and remembrance in the late Middle Ages and early modern times.

In spring 2007, with the support of the village of Kapellendorf and the Gotha District Church Office, the parish was able to re-slate the roofs of the tower and the choir room.

In 2009, with the support of the village, the longhouse was also roofed in line with its listed status.

A Luther tree was planted in front of the church in 2017.

On June 1, 2003, a new, electronic organ was consecrated. The previous instrument had been improperly removed and stored during renovation work in 1976, causing irreparable damage. The people of Kapellendorf therefore decided to purchase an electronic organ. The sampled tones sound "true to the organ" from loudspeakers located behind the old organ case.

In addition to the bronze bell made by Gebrüder Ulrich (Apolda) in 1787, two cast iron bells made by Schilling & Lattermann (Apolda and Morgenröthe-Rautenkranz) in 1920 ring in the tower. Two bronze bells are planned for the latter.

A printed theological work from the Reformation period dating back to 1566 has been preserved. It comes from the estate of Simon Hartung, one of the first pastors in Kapellendorf, and contains a detailed library list of the time with many works by leading Protestant theologians.