On 13 September 1494, as part of a campaign to staff the Irish judiciary with Englishmen of proven loyalty to the Tudor dynasty, he was appointed Lord Chancellor of Ireland under Sir Edward Poynings, in which capacity he made the opening address at the Drogheda Parliament of December 1494.
When Poynings was recalled in January 1496, Deane was appointed his successor as Deputy Governor, but sour relations with the local clergy led to his removal in August of the same year.
[2] On 13 April 1494, he was appointed Bishop of Bangor (confirmed by the Pope in July 1495), where he engaged in rebuilding the fortunes of the diocese after the rebellion led by Owain Glyndŵr.
On 7 December 1499, Henry VII appointed him to the much more significant bishopric of Salisbury, confirmed by the Pope on 8 January 1500.
On 13 October 1500, after the death of the Chancellor, Archbishop John Morton, Deane was appointed Lord Keeper of the Great Seal, which held until 27 July 1502.