Tragedy struck the family in 1694 when John's younger son Henry was killed in a brawl with an English merchant in Lisbon.

[3] John established good relations with King Pedro II which were to be of value later in negotiating the Methuen Treaty, but was required to return to England on his appointment to the Board of Trade, while his son Paul remained in Lisbon to act as deputy envoy.

The Irish Parliament during his tenure as Lord Chancellor dealt with issues of security, trade, whether to honour (even in part) the articles of the Treaty of Limerick, and the Penal Laws, all of which were the subject of intense controversy and heated debate.

He was required to spend more and more time in England, leading to complaints that he was an absentee Chancellor; Elrington Ball in his history of the Irish judiciary remarked that though he held office he could hardly be said to occupy it.

[1] Methuen complained that his reputation had been ruined and contemplated resignation, due to his belief that King William III had lost confidence in him.

He described most of the Irish judges as being men of such high reputation that "no one complains of them";[6] but made a significant exception for Methuen, who he remarked seems to be out of vogue.

[2] Until 1703 he was permitted to retain the Irish Chancellorship, although he never sat as a judge again, but in that year the Lord Lieutenant of Ireland, James Butler, 2nd Duke of Ormonde, insisted on his dismissal, saying bluntly that "he would not have him".

Paul in his father's absence ultimately concluded the Treaty on 16 May 1703, a step of great significance in the War of the Spanish Succession.

[10] Methuen in later life increasingly suffered from gout and rheumatism; his health failed and he died at Lisbon, while still in office, on 2 July 1706.

Despite his undoubted skills as a diplomat, Methuen was a controversial figure, who made many enemies, including Jonathan Swift, who dismissed him as "a profligate rogue without religion or morals, cunning enough but without abilities of any kind".

His speech on Fenwick's attainder shows him to have been a gifted lawyer, but as a judge, he was not highly regarded in Ireland, although his admirers maintained that he made several necessary reforms to the legal system.