The west window is also early 15th century. The south aisle was added in the early 16th century. The church';s roof, pews, font, pulpit and east window were restored in 1864 after a period of neglect. The east window received stained glass in 1889.
The church's graveyard is surrounded by a limestone wall, with a village pinfold on its north side. The pinfold was used by the village pinder to impound loose and stray animals, released on payment of a fine by the animal's owner.
The Scrooby Separatist Church was established by William Brewster at Scrooby manor house in about 1606. Meetings were held in secret to avoid arrest. Principal members were Richard Clyfton, John Robinson and William Brewster. There were also other locals who held similar Separatist views; for example, William Bradford of Austerfield had been orphaned as a child, and lived with Brewster at Scrooby. In 1620 Brewster left England on board the ship Mayflower as the elder of the Separatist group later known as the Pilgrim Fathers. They became the founders of Plymouth colony in New England.