The oldest reference to a church in Woerden dates from 1202. In that year a wooden church was destroyed by fire. This church had been standing on the site of a former Roman castellum, and a new church was built on the same location later in the 13th century, probably of tuff.

In ca. 1372 work began on the construction of the current tower. It's in a simple and robust Gothic style and is the only remaining part of the second church. In ca. 1450 a bigger nave with a transept and a new choir were built, both in late-Gothic style. The church was now a three-aisled cruciform pseudo-basilica.  In ca. 1500 the choir was extended with an ambulatory and two radiating chapels. In the mid-16th century the southern entrance was transformed into a new building which was used for the storage of archives.

In 1566 the church became protestant. Unlike most other churches that were confiscated by protestants in that period the St. Petrus became Lutheran first, not Calvinistic. When in 1591 calvinism became the official religion in Woerden the church also became reformed.

In 1672 the church was badly damaged by fire. Three years later it was rebuilt, but with a simplified roof on the ambulatory. In the 19th century the walls were covered with a coat of plaster on the outside. This was removed during a big restoration in 1980-1983. The southern radiating chapel was transformed into a portal in 1865 and has remained so.