James Bathe, later Chief Baron of the Irish Exchequer and a trusted Crown servant for thirty years, faced Cowley's hostility from early in his career.
[6] In the 1530s Robert and his brother Walter Cowley engaged in a power struggle with Patrick Barnewall, the Irish Solicitor General, who also had considerable influence with Cromwell.
Cowley's influence declined after the downfall and death of Cromwell in 1540: Henry VIII distrusted him, and like many leading political figures of the Pale he quarrelled with Sir Anthony St. Leger, the Lord Deputy of Ireland.
In 1541 Cowley unwisely went to London without official leave: he was promptly denounced for sedition, imprisoned in the Fleet Prison and deprived of office.
His letters to Cromwell, particularly those which detail his efforts to destroy Patrick Barnewall, show him in an unattractive light, and historians have described both Robert and Walter as "ambitious mischief-makers".
Henry was an ancestor of Richard Colley, who adopted the surname Wesley, was created Baron Mornington and was grandfather of the 1st Duke of Wellington.