The village name was anciently Isenhampstead. There were two villages here, called Isenhampstead Chenies and Isenhampstead Latimers, distinguished by the lords of the manors of those two places. It was in the late medieval period that the prefix was dropped and the two villages became known as Chenies and Latimer.
Near this village there was once a royal palace, where both King Edward I and King Edward III were known to have resided. It was Edward I's shield bearer, Thomas Cheyne, who first gave his name to the village.
In 1494 the incumbent Lady Agnes Cheyne gave the manor of Chenies in her will to the Earl of Bedford. In 1560 the house was restyled by Francis Russell, 2nd Earl of Bedford, who had made it his principle home. In 1570 Queen Elizabeth I was entertained here.
Several paper mills were once established in Chenies, operated by the River Misbourne, which flowed here from further west in Buckinghamshire.