Gordon was serving with the Mediterranean Fleet when he abruptly deserted his post in May 1745; this coincided with Charles Stuart putting in motion his plans for a Scottish rising.

John Bissett, commented that Gordon "met so many old friends and acquaintances engaged in the rebellion, who all laid oars in the water to gain him; and this indeed was no hard matter to a forward young lad like him, especially as he was to have a Feather in his cap, and to be made Lord Lieutenant of Aberdeenshire and Governor of the towns of Aberdeen and Banff".

"[6] He briefly experimented with quartering Highlanders on those who refused, but then moved on to threats of burning property; Bissett noted that the firing of one house in a district "soon had the desired effect".

With his regiment up to strength, Gordon organised the defence of Aberdeen before moving against the government's Independent Highland Companies under the Lord Macleod.

He nominally led one column of Jacobite troops and Avochie another, though in reality it appears that active command was delegated to Major Cuthbert, brother of the laird of Castlehill and a regular in the French Royal-Ecossais, who "did all the business".

[11] In 1749 he was one of six prominent Scots appointed to a commission sitting in Paris to examine the claims of Scottish refugees to financial assistance from King Louis XV; the same year a French government memo recorded that Gordon was barely on speaking terms with Charles, suffered from attacks of vertigo, and was "often disturbed".

[14] His name was remembered in Scotland in a popular Jacobite air, "Lewie Gordon"; James Hogg identified its author as the Catholic theologian Alexander Geddes (1737–1802).