In 1588, Ó Duibheannaigh was committed to Dublin Castle. Failing to convict him of any crime punishable by death, Lord Deputy William Fitzwilliam sought authority from William Cecil, 1st Baron Burghley to "be rid of such an obstinate enemy of God and so rank a traitor to Her Majesty as no doubt he is". He lay in prison until November 1590, being then released ostensibly on his own petition but doubtless through policy. He was protected by Hugh O'Neill, Earl of Tyrone until 1607 (see the Flight of the Earls), and escaped arrest until the middle of 1611, when, almost eighty years old, he was taken while administering Confirmation and again committed to Dublin Castle. His execution was at the personal wish of the Lord Deputy of Ireland, Sir Arthur Chichester, who was vehemently anti-Catholic, and seems to have been rather against the wishes of the Government as a whole.