The original church was dedicated to St. Mary, and was changed to St. Peter after the Reformation. It was the Saxons who raised the first church on the site of St. Peter's Church today, just before the Norman Conquest. The church was completed sometime between 1090 and 1130, and consisted of the tower, nave and chancel built of rubble, puddingstone, and Roman bricks topped by a thatched roof. The North and South aisles were added in the 14th century. The upper part of the tower collapsed in the 1500s and was rebuilt with red bricks and buttresses, and topped with a new third story. The chancel was also completely rebuilt in that era. The thatch roof was removed in the 1700s and replaced with tiles.

The Black Death (bubonic plague) ravaged this area between September 1348 and September 1349. Records of deaths were not kept, but it is believed that during this period almost half the population of Boxted succumbed. It is believed that an unmarked communal grave was created on the north side of the church (next to the Essex Way), containing 32 bodies.

Boxted seemed to have been in the vanguard of the Puritan movement in the 1500s. Between 1620 and 1640 many people left this area of East Anglia as part of "The Great Migration" to New England in America, primarily seeking to escape religious persecution. The Boxted parish numbered many Puritans among its people, including the vicar of Boxted, Rev. George Phillips, and his family, who left in 1630 and established the Congregationalist Church in Watertown, Massachusetts. But Boxted remained an extreme Puritan community that experienced much trouble in the village following the Restoration.

All of the above information is learned from the excellent book by Douglas Carter, "Boxted: Portrait of an English Village" (C.L.W. Publishing, Boxted; 2006). On page 80 we also find this helpful history:

"The earliest churchyard gravestones were erected in the 17th Century by yeomen, husbandmen and craftsmen in imitation of their superiors who were buried inside the church. These early gravestones are found on the South side near the church porch. The North side was regarded as the 'Devil's side' and was used for the burials of excommunicants, suicides and the unbaptised. This superstition declined in the 18th Century but, to this day, the North sides of churchyards are usually much smaller than those on the South."