However, in 1647 a Parliamentary commission (or visitation) was set up "for the correction of offences, abuses, and disorders" in the University of Oxford. Nathaniel Brent was the president of the visitors. After Thomas Fairfax had captured Oxford for the Parliamentarians in 1648 and Brent had returned from London, Greaves was accused of sequestrating the college's plate and funds for king Charles. Despite a deposition from his brother Thomas, Greaves had lost both his Merton fellowship and his Savilian chair by 9 November 1648. Many of his books and MSS disappeared after his rooms were rifled by soldiers, although his friend John Selden managed to recover some of them. However, Greaves was not actually deprived of the professorship until August 1649.