In 1639, at the commencement of the Scottish rebellion against the Crown, Lord Winton left the country and waited upon King Charles I after the pacification of Berwick to offer his loyal services, for which the rebels did him great injury; and thereafter all through the Civil Wars he was constantly harassed:
"Cromwell and his army of cavalry domineered in all parts where they came, and in especial about Edinburgh, and in East Lothian. The good Earl of Winton, to whose well-furnished table all the noblemen and gentlemen had ever been welcome, was pitifully abused by them; his fair house of Seaton made a common inn; himself threatened to be killed, if they had not whatsoever they called for; his rich furniture and stuff plundered, and all the enormities that could be offered by Jews or Turks to Christians, he suffered daily; and when he complained to those of our nobility who now rule all, he got no redress, but ordered with patience to give them whatsoever they called for."
When James Graham, 1st Marquess of Montrose was in command of the Royal forces in 1645, the Earl's eldest son, George, Lord Seton, joined him, and was taken prisoner at the disastrous battle of Philiphaugh and remained long "in hazard of his life". George, Lord Seton died before his father, in 1648. George, Earl of Winton, entered into the 'Engagement' for the rescue of His Majesty in 1648, giving £1000 sterling to the Duke of Hamilton, the commander-in-chief, in free gift for his equipage. Like his father, the Earl suffered a long series of petty persecutions from the Presbytery of Haddington because of his allegiance to the Roman Catholic faith. For instance, on 4 November 1648, the Presbytery ordained "a purge the House of Setoun of 'Popish servants', and to proceed both against them and against the Earl of Wintoun if he protect or resset them after admonition." When King Charles II came to Scotland in June 1650, the Earl of Winton was in continuous attendance on him, and continued with His Majesty until November. He then went home to Seton to prepare for his attendance at the Coronation, but died on the 17th of December of that year.
By his second wife, Elizabeth, only daughter of John Maxwell, 6th Lord Herries of Terregles, Lord Winton had six sons and six daughters, of whom:
William
Christopher, regarded as a great scholar. These two brothers and a preceptor, while going "on their travels abroad, were cast away at sea upon the coasts of Holland in 1648".
John
Robert
Ann, married at Winton House in April 1654, to John Stuart, 2nd Earl of Traquair, by whom she had three sons and one daughter, Elizabeth, who died "a brave hopeful young lady", at twenty years of age. It is said that when Lord Traquair married Lady Anne Seton, the Covenanters made him stand at the kirk door of Dalkeith in a sack, for marrying a papist.