St. Kunibert is the youngest of the Twelve Romanesque churches of Cologne and was consecrated 1247, one year before work on the Gothic Cologne Cathedral began.

A small church located at a burial ground north of the Roman city was founded or renewed by Cunibert, ninth Bishop of Cologne. Cunibert was also buried there. After 690 the Two Ewalds were buried in the church as well.

The church was originally dedicated to Saint Clement, but Cunibert was adored alongside him at least since the ninth century and a monastery Saint Kunibert was first mentioned in 866. Around the middle of the eleventh century the direct predecessor of the current church was built. Later a parish with the dean as parson was allocated to the monastery. The church became a pilgrimage site after the Canonization of the Two Ewalds in 1074 and of Cunibert in 1168.

Between 1210 and 1215 the erection of the current building started. The choir was finished 1226 and the church consecrated in 1247. Until 1261 a transept and a tower were added to the west.

The monastery ceased to exist in 1802 as a result of the secularization under Napoleonic reign and the monastery buildings were eventually torn down in 1821. However the church remained in use by the local parish.

The western spire collapsed during a storm in 1830 for static reasons, as this tower was not part of the original plan and the structure of the building was not designed for it. Reconstruction was completed in 1860.

The church suffered severe damage during the Second World War. The roof was destroyed by fire. The western tower was destroyed again by a bomb. Reconstruction of the choir and nave were finished 1955, and rebuilding of the transept and western tower were finished in 1985.

The original shrines of Cunibert and The Ewalds were destroyed during secularization and only the wooden cores with the relics remained. Today's shrines in the crypt are from the second half of the 19th century and there seems to be no evidence of the original graveyard.

The eight medieval glass windows in the apse area were made between 1220 and 1230. The upper three windows show Saint Clement, the original patron of the site, the Tree of Jesse and Saint Cunibert. The windows of the lower band show Saint Ursula, Saint Cordula, Saint Catherine, Saint Cecilia and John the Baptist.