This church has a long history of alterations. Originally a single-aisled tuff church in Romanesque style, which in the mid-13th century was extended with a transept and a new rectangular choir. At first the church was consecrated St. Willibrord, later the name was changed to St. Michaël.
Ca. 1300 the construction of the tower started, which lasted for most of the century. This tower has a rectangular base, and is in a style that clearly illustrates the transion from Romanesque to Gothic. The top of the tower is unique. The saddle roof is uncommon for this part of the country, but the way its ends are sloped is without an equal. At the east side of the roof is an extension for the carillion, added in 1601.
The porch which runs from north to south is more common, although mostly in the former county of Holland, to which Oudewater belonged at the time. This is probably for safett reasons, the river Ijssel running very close to the church.
At the end of the 14th century a closure of five sides was added to the choir. In the early 15th century the choir was flanked with straightly closed side-choirs with big windows in their east ends, resulting in a hall-choir. At the same time a transept was built of the same width as the enlarged choir. In the mid-15th century side-aisles were added. These were of equal height and width as the nave, making the building a three-aisled hall-church. Because of space limits, the southern side-aisle is slightly shorter, which resulted in a diagonally positioned facade.
In 1572 the St. Michaël became a protestant church, after the town had chosen the side of the prince of Orange against the king of Spain. The church survived the big fire of 1575, when Spanish troops destroyed most of Oudewater and killed half of its population. In 1732 the gables and roofs of the transept were removed. During a restoration in 1960-1967 these were rebuilt, while a coat of plaster was removed from the entire outside of the church.