Middleton had served in many parts of the British Empire by 1884 when he accepted the position of general officer in command of the Canadian militia.

In 1885, Middleton led a militia force to the northwest to suppress a Métis and First Nations uprising. He personally led the main force toward the hotbed of trouble at Batoche. The Métis under Gabriel Dumont attacked Middleton and his men along the way. Although the Métis won, they failed to decisively defeat Middleton. He made it to Batoche with forces outnumbering the Métis by three to one. But Middleton could only gain victory after his opponents ran out of ammunition. With the Métis defeat, Poundmaker surrendered to Middleton on May 26, 1885.

For his role in the northwest, the Canadian Parliament rewarded Middleton with $20,000. Queen Victoria knighted him.

He resigned in 1890 after a Parliamentary committee criticized him for misappropriating the furs of a Métis named Charles Bremner. Middleton lived out his remaining years in England where he'd obtained the post of keeper of the crown jewels.