A Neolithic polished flint axehead was probably found near the Mission Hall but the earliest evidence for human activity in Lower Winchendon is a Mesolithic flint tranchet axehead that was found in the grounds of the Manor House when the swimming pool was built in the 1970s. Roman pottery was also found in this trench. A Roman road is thought to pass through Lower Winchendon. Roman and medieval pottery was also found south-west of the church, suggesting some activity along the line of the road in the Roman period. Some more Roman pottery was found on fields south of Whaddon Field Farm. Roman, Saxon and medieval pottery were found near Manor Farm. An Early Saxon cremation burial was found during ditch recutting north-west of Winchendon Hill Farm in the 1950s. Nearby two ring-ditches can be seen north-east of Cedarwood on aerial photographs and may be associated with the burial.
Lower Winchendon (also known as Nether Winchendon) was recorded in Domesday and was part of Bernwood Forest from before this time. Bernwood had been a hunting forest from the time of Edward the Confessor. It grew to its largest extent under Henry II. The whole area was not covered by woods; in the medieval period a forest was a place where deer roamed for hunting and so included open land, villages and fields. All those who lived in the forest were not allowed to hunt or even gather wood without a special licence from the king. Bernwood Forest was finally disafforested in the reign of James I in 1635, although it had been shrinking in size since the time of King John (1199-1216).
Lower Winchendon was probably bigger in the medieval period as earthworks of the larger village are known east of the church and in the park of Nether Winchendon House. Domesday records a fishery and watermill in Lower Winchendon and the latter continued working, probably with many alterations, until 1911. The mill-house still remains, though it dates to the 19th century. It was a papermill in the 19th century before being converted back to grain.
The oldest surviving building in Lower Winchendon is St Nicholas’ church, dating back to the 13th century, though it was mostly rebuilt in the 14th century and has a 15th century tower. Nether Winchendon House was built in the 15th century and belonged to Notley Abbey before it was improved during the 1530s after being given to Sir John Dauncy on the dissolution of the monasteries. There may have been an earlier house on the spot as medieval dressed stone and pottery has been found in the grounds. It was known as Winchendon Priory, presumably because of its former association with Notley Abbey. There are records of a dovecote attached to the house in the 16th century. Manor Farm was probably the site of the manor house that belonged to the Knollys family and dates back to the 16th and 17th centuries. One of the barns was built in the 17th century but reused timbers from a 15th or 16th century building.
Lower Winchendon is part of a small number of villages that contain witchert built houses. Witchert is a local building material made from the limestone peculiar to this locality. The Bear House is 18th century and made of witchert; Hillside is a 19th century example of a witchert house. Winchendon Hill Farm is not witchert, and dates back to the 17th century. One of the timber-framed barns at the farm is also listed. The Old Parsonage and Ashtree House are both 17th century and timber-framed, suggesting that witchert may have been more common in later centuries, or perhaps that earlier witchert buildings have not survived in Lower Winchendon.
The Victorian period brought industry to Lower Winchendon. There was a lime kiln at Marsh Farm in the 19th century. As well as the watermill, the field name Millfield suggests the site of a windmill a supposed predecessor of Cuddington Mill which was just to the east.