In 1640 Honywoood was appointed to the college living of Kegworth, Leicestershire, but he did not reside there; and when the First English Civil War threatened Cambridge at the beginning of 1642, he crossed to the Low Countries.
In 1643 Bainbridge ineffectually wrote to Honywood urging him to return, so as not to exceed the statutable limit of absence, which would defeat his wish that Honywood should succeed him as master.