On Eudo's death the manor became property of the Crown and was attached to the Barony of Lindon [Lincoln].

At some time before 1377 Agnes, wife of Henry de Huntingfold was dispossessed by William de Brounsford who alienated the manor to Nicholas Westerdale and others who obtained a licence in 1386 to convey it to Warden Abbey in exchange for the abbey's granges at Ravensholt and Burdon in Cambridgeshire.

In 1658, one of these parts was conveyed by Nathaniel Parcell to Jasper Edwards, Chief Registrar of the Court of Chancery.

During the next hundred years the manor seems to have been reconstituted and appears in the ownership of Samuel Cockayne and Bromsall Throckmorton.

Since April 2011, the title of Lord of the Manor of Thorncote has been held by Ian J. Wilkinson of nearby Peterborough, Cambridgeshire.