By 1760, Sinclair was at Oswego, New York, where he was promoted Lieutenant, and involved in the Seven Years' War. His battalion were part of the force heading to attack Montreal under the command of Major-General Amherst. They captured a French brig near Fort Lévis and Sinclair was given command. After Amherst's force captured Fort Lévis in what became known as the Battle of the Thousand Islands, Sinclair was assigned to the area for the rest of Amherst's campaign. In 1761 he exchanged into the 15th Foot in order to stay in the area.
This contact with the Great Lakes attracted Sinclair and he was able to change his commission to serve on the lakes. He started out commanding ships on Lake Ontario but, in 1764, he was moved to the upper lakes where he served until 1767. In 1767, he was removed from active service at Fort Sinclair, which he had built in 1764 under orders from Colonel John Bradstreet.
In 1769, he went to England on a recruiting trip and tried to be reassigned to the Great Lakes. He was promoted Captain in 1772, but retired to his home in Lybster at half-pay later the same year.
However in 1775, his wish to return to the Great Lakes was granted with an appointment as lieutenant-governor and superintendent of Michilimackinac. He was thwarted in taking up his post by unrest in the thirteen colonies and he reached his posting via Nova Scotia and Quebec in 1779. He almost immediately began to move Fort Michilimackinac and its community to Mackinac Island . There, after an extreme effort and large expense, Fort Mackinac was occupied in 1781. In 1781, Sinclair joined the 84th Foot. By 1782, when he was promoted Major, his expenses had come under investigation and he returned to Quebec to untangle his finances.
Sinclair was not able to clear up his problems but he was allowed to return to Lybster. He continued to work on clearing up unpaid bills and ended up in debtors prison for a time. He never recovered financially and spent his remaining years on his estate drawing his half pay from the military and also from his time as lieutenant-governor of Michilimackinac. The latter must have been a reminder of his brief position of power in that endeavour.