He was a staunch friend of Hugh O'Neill, Earl of Tyrone, and hosted the negotiations that led to the Treaty of Mellifont in 1603 and the ending of the Nine Years' War.
However, after Tyrone's flight to the Continent in 1607, he was the target of vehement attacks by his enemies, especially the volatile and unreliable Christopher St Lawrence, 10th Baron Howth, with whom he had quarrelled bitterly, despite being related to him by marriage.
Lord Howth accused Moore of treasonable dealings with Tyrone, and pressed the charges with such vigour that the Lord Lieutenant of Ireland, Sir Arthur Chichester, who had originally laughed at them as "too absurd even to charge a horse-boy with, let alone a knight", felt obliged to place Moore under house arrest.
Moore admitted that on the eve of the Flight of the Earls, Tyrone had visited him at his home, Mellifont, but he firmly denied any imputation of treason.
Lord Howth, summoned before the Irish Council, refused to produce any evidence of the alleged treason, on the ground that since Moore was himself a Privy Councillor, that body was clearly guilty of bias, while his bizarre claim that he had seen Moore trying to raise the Devil did nothing to enhance his credibility.