On the outbreak of the civil war in 1639 he accepted a command under General Alexander Leslie, and was present in the following year at the taking of Newcastle.

After his elder brother's death he returned home to assist his now disabled father, and served on the committee for war of the Stewartry of Kirkcudbright, from whom he presented a petition to parliament in 1648.

Owing to his strict adherence to his religious principles he was exempted from the act of indemnity granted by Charles in 1662 until he should pay a large fine of £3,500; while about the same time he and a number more were pursued by James, earl of Queensberry, to pay their shares of the damage sustained by that earl in a raid which they had made in 1650 upon his Drumlanrig Castle.

For this "seditious carriage" he was called before the privy council, but they do not appear to have found that his conduct amounted to a punishable crime, and therefore, on the 24 November 1663, he was summoned upon the more comprehensive accusation of keeping conventicles and private meetings in his house; and, a little more than three months later on 1 March of 1663/4 — until the year 1751, England did not mark the change in year until March 25, so March 1 was still "1663" on the English calendar and 1664 on the Gregorian calendar and in some nations where the Julian calendar was still in effect — Gordon was found guilty, upon his own confession, of having been one at three several conventicles, when Mr. Gabriel Semple, a deposed minister, preached — one in Corsack wood, and two in the wood of Airds; of hearing Mr. Robert Paton, likewise a deposed minister, expound a text of Scripture, and perform divers acts of worship in his mother's house; and of allowing Mr. Thomas Thomson, another of the same kind, to lecture in his own house to his family on a Sabbath day — for these offences, and because he would not engage never to repeat them, he was banished forth of the kingdom, not to return under pain of death.

[7][8][9] A month was allowed him to make his preparations, during which he was ordained to live peaceably and orderly under a penalty of £10,000, or enter himself in prison.

His house at Earlston was frequently made a barrack for the troops employed in hunting down the covenanters, and he himself had to construct a secret and safe hiding-place in the depths of the forest of Aird.

His body was secured, and buried by his sister-in-law, the wife of Sir John Harper of Cambusnethan, in Glassford churchyard, Lanarkshire, where a plain pillar was erected to mark the spot of interment.

They were married on 26 October 1648, and had issue thirteen children, most of whom died young, only three sons and one daughter reaching maturity.