Following the accession of Elizabeth I, rumours circulated that the queen would like to marry her master of the horse Robert Dudley, later earl of Leicester in emulation of her cousin and Stokes.
[3] The Duchess of Suffolk died in 1559, leaving Stokes a life interest in most of her land.
[3] In 1564 Stokes was classified by his bishop as a committed Protestant, and he served on local commissions to enforce attendance at church and to discover recusants.
[3] In October 1571 his step-daughter Lady Mary Grey asked to be allowed to live with her step-father at Beaumanor.
[3] In Warwickshire he became notorious for the damage caused to the church at Astley, where he pulled down the spire rather than repair it and stripped the roof of its valuable lead.