Also unofficially known as Nieuwstadkerk, the church of St. Johannes de Doper, as this official name suggests, was returned to the catholics after they were granted freedom of religion. Not many medieval churches in the northern half of the country were returned to their rightful owners but this one did, in 1806 to be precise. After ten years of much-needed repairs and restorations it could be consecrated again in 1816. The protestants kept the other medieval churches, including the prestigious St. Walburgis.

The St. Johannes was built for the parish of Nieuwstad, which was founded before 1272. Nieuwstad was a settlement just outside the walls of Zutphen, ruled by its own local government. In 1313 Nieuwstad became part of Zutphen. Of the original church nothing remains; the oldest parts of the current church, the three lower segments of the tower, the central aisle of the nave and the first trave of the choir, date from ca. 1300. The tower was heightened in ca. 1439, the spire dates from 1439-1442. The choir was enlarged in the mid-15th century. In the same period the first three traves of the southern side-aisle were built, followed shortly after by the fourth. The northern side-aisle was added in ca. 1500. The formerly aisleless church was thus rebuilt into a hall-church. After a fire early in the 16th century the roofs were replaced and both side-aisles were lengthened with a fifth trave. During a restoration in 1927-1928 a portal was added to the western facade of the southern side-aisle. The sacristy at the south side of the choir probably dates from the same period.