The origin of the church building stems from the 9th century, during which a women’s home of the same name was founded at the site, during the reign of Archbishop Willibert in 870-888.

[3] Previously, it was suggested that the first Cologne Cathedral stood at the site, but archaeological evidence has since ruled out this possibility.

From documentation of the home in 965, it is known that Bruno the Great, archbishop of Cologne, designated 50 pounds of silver for the completion of the church building.

Through resources originally designated for another church, the interior of St Cecilia's was renovated during the late 15th century.

Though it is currently used mainly as museum of medieval art, the church celebrates two masses each year, one at Christmas and the other on the feast day of St. Cecilia.