Chalton was historically a hamlet of Blunham|. Care must be taken not to confuse it with another, bigger, Bedfordshire hamlet called Chalton which is a hamlet in the parish of Toddington. The name first appears in the 11th century as Cerlentone and was recorded as Cherleton in the 13th and 14th century and means "calf farm". Since 1866 Chalton has been part of the civil parish| of Mogerhanger|, itself once part of the ancient parish of Blunham

The Domesday Book| of 1086 recorded that Chalton was owned by Adelaide, wife of Hugh de Grandmesnil. It formed the manor later known as South Mills and also included part of Mogerhanger and had ten hides and land for ten ploughs. The population was more significant than in some parishes, as there were 16 villagers, 9 smallholders and 2 slaves, a total of 27. This figure should be multiplied by about a factor of four to allow for women and children giving a total population of around a hundred. A mill|, naturally, is recorded. Before the Conquest the Manor had been held by earl Tosti from King Edward the Confessor. Tosti was the brother of King Harold and was killed at Stanford Bridge in 1066, fighting against his brother and for King Harald of Norway. The Domesday Book noted that the Manor was an outlier of Potton before 1066 rather, than as one might have expected, of Blunham.

The earliest recorded tenant of the Manor was William Lovel who held half of it at the beginning of the 13th century and he was succeeded by the de Harcourt family. At some time between 1319 and 1347 the Manor passed to Robert de Holwell, John Malyns, Nicholas Crowe and John de la Hay. By 1469 the Manor had become the property of George Gascoigne of Cardington who then sold it to John Maningham who transferred  it to John Mordaunt and John Vynter in 1484. It next appears in 1549 being alienated by John Aleyn to Humphrey Brown and others. The next mention of it occurs in 1679 as property of Thomas Cheyne who then conveyed it to Thomas Bromsall. the Bromsalls appear to have sold the Manor to the Astell family who then sold to the Thorntons. In 1864 the last of the Thorntons died without issue and the new owners were the Dawkins family and it survived in their ownership into the twentieth century.

A Manor of Chalton is recorded in the 17th century. It followed the same descent of ownership as South Mills Manor.