He was taken prisoner at the Siege of Grand Pre during Father Le Loutre's War in Nova Scotia (1750). The Mi'kmaq militia captured Lieutenant John Hamilton and eighteen soldiers under his command (including British officer John Handfield's son), while surveying the fort's environs. He was imprisoned in Quebec for two years before he was able to negotiate for the freedom of himself and 60 other prisoners.Murdoch, p. 204 He was helped to gain his release by both his father Otho Hamilton and his father-in-law William Shirriff, both of whom were members of the Nova Scotia Council. Jean-Louis Le Loutre had paid Mi'kmaq ransom for Hamilton's release. He also was traded for the daughter of an Indian chief that John Gorham had imprisoned in Boston at his own residence with his daughter. Upon his return he married his second wife, daughter of his commander John Handfield.
