The parish has five separate entries in the Domesday Book of 1086:

• Remigius, the Bishop of Lincoln held three hides and half a virgate. His tenant was William de Caron and the holding included three villagers and two slaves. The holding had belonged to Alwin Devil under King Edward the Confessor and had been worth £4 but, by the time of Domesday had been reduced to £1 by the depredations of William I's army as it marched north to put down rebellion. This land later became known as Clifton Manor
• The Abbey of Saint Benedict's, Ramsey [Cambridgeshire] held one hide of land, tenanted, still in 1086, unusually, by a native - Leofwin, who had held it from the Abbey before the Conquest, its value had halved in the interim from 20/- to 10/-. The history of this land after it is last mentioned in the 1180s as belonging to Ramsey Abbey, is not known.
• A third slice of Clifton was held by Eudo, son of Walter and consisted of 6½ hides tenanted by William de Caron. This holding included 9 villagers, 1 smallholder and 3 slaves as well as two mills valued at £2 and 150 eels (it is possible these were watermills on the River Ivel and may have been the site of the later Shefford watermills). Before the conquest the manor had been worth £6 and had been held by Wulfmer of Eaton [Socon?] and three Freemen. The value in 1086 was £4. This manor was later held by the Prior of the Order of the Knights Hospitaller of Saint John of Jerusalem.
• Nigel d'Aubigny held the fourth slice of Clifton, his tenant, again, being William de Caron who had two hides. Before 1066 four freemen had been holders and the holding had been worth 20/- but was now worth just 10/-. This land later became known as the Manor of Clifton Lacies.
• The last piece of Clifton recorded in Domesday was held by Countess Judith and her tenant Alwin, again a native sounding name. This holding was of just one hide and had previously been held by Edward the Confessor's man Wulfric and had been worth 10/-, reduced in 1086 to 5/-. This land was later owned by Old Warden Abbey.

A guess at the population of Clifton on 1086 can be made from noting that the combined numbers mentioned as being parts of the various holdings were twelve villagers, one smallholder and five slaves - eighteen people, the heads of household. It seems reasonable to multiply this figure by at least four to get a total of all the women and children too, so the total population may have been about 75 to 80.