Not a lot of prehistoric material has been found in Shabbington, but one flint flake that may date to anywhere from the Mesolithic to the Bronze Age was found in the spoil of a ditch recutting on Aich Hill and a Neolithic polished flint axe-head was found in a ditch south-east of Peppershill.
Iron Age to Roman ditches were recorded in a watching brief on a gas pipeline north-east of the village in 1976. A little Roman pottery has been found north of the church and west of the village. A Roman road from Dorchester-on-Thames through Fleet Marston is supposed to pass through Shabbington and ford the River Thame. Small scale excavation during topsoil stripping for a new gas pipeline south-east of Peppershill carried out by Thames Valley Archaeological Services in 1999 identified a pit, a ditch and 3 cremation unurned cremation burials of Roman date. A deposit of cremation pyre debris may possibly be of Iron Age date.
An undated skull dredged from the River Thame could be of any date, but late Saxon pottery that was also found with it may suggest it was part of a burial deposit of this date that was eroded out by the river. Shabbington is recorded in Domesday and was part of Bernwood Forest from the late Saxon period, too. 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).
Shabbington manor was based somewhere near the church, possibly on the site of the former farmhouse south of the church. There were also medieval village earthworks around the church, but these were destroyed by a new housing estate. Medieval fishponds were also recorded north of the church, and they were mentioned in Domesday. Ridge-and-furrow survives around the parish, the remains of the medieval farming technique.
The church is the oldest standing building, dedicated to St Mary Magdalene, incorporates some 12th century fabric but there was extensive rebuilding in the 14th and 15th centuries. A mound was recorded south of the church, which may have supported a medieval windmill. The medieval watermill, recorded in Domesday, is recorded on historic maps where the Old Fisherman pub is now. The Barley Mow pub was turned into a farm called Duke’s Close and that was pulled down in 1978. The second oldest standing building is Village Farm, which dates back to the 16th century. The School House and Old School used to be, as can be guessed from the names, the village school. The buildings date back to the 17th century. Other listed buildings in the parish date to the 17th and 18th century.