The history of Benschop began in the 12th century, with the reclamation of the Lopikerwaard. Benschop grew to eventually become an 8 kilometers long ribbon of mainly farms on both sides of the Benschopper Wetering canal, with at its center a square on which in the 13th century a church was built, dedicated to St. Nicolaas. Of this first church the lower part of the tower remains. The choir and transept were built in the 14th century while the original nave was probably replaced by a three-aisled pseudo-basilican one after that.

After 1450 the tower was heightened with its current upper part which features, by then quite archaic, Romanesque details. In ca. 1500 the pillars were removed from the nave and its walls were raised, resulting in the current wide aisleless space with wooden vaults.

In 1578 the church became a protestant one. The building remained intact safe a few smaller changes, the biggest of which was the replacement in 1803 of the sacristy by a consistory and the removal of the traceries in the windows in 1839. When in 1956-1959 the church was restored the sacristy was reconstructed, based on a engraving from 1744, and new brick traceries were added.