John McClellan was deeply involved in the religious and political struggles of his time, which centered around the conflict between the Presbyterian Covenanters and the Royalists during the Wars of the Three Kingdoms.
In February 1649, he was appointed Colonel of Foot for the counties of Galloway, Ayrshire, and Renfrewshire, and was tasked with raising a regiment of soldiers to fight in the ongoing conflict.
Initially, the regiment was to have 800 men, but McClellan struggled to recruit sufficient forces, and only a fraction of the expected soldiers was raised.
Despite these setbacks, McClellan's forces fought in the Irish campaigns of 1649, where they faced severe defeats, including a disastrous engagement at Lissnagerry, Ulster, which nearly wiped out his regiment.
In 1649, he corresponded with John McClellan, a minister in Kirkcudbright, discussing the contentious issue of church patronage, which was a subject of considerable debate at the time.
The correspondence indicated McClellan's commitment to a Presbyterian form of church governance and his disdain for the increasing influence of royalist and Episcopalian factions.
Following his death, his widow Ann Maxwell received a liferent (a right to the use of the deceased's property for life), and the remainder of his estate was eventually passed on to his son, William McClellan, who succeeded him as the 4th Lord Kirkcudbright.