In July 1884 he was appointed commander of the Canadian Militia, and to him fell the task of organizing and leading the expedition during the North-West Resistance of 1885. The organization was accomplished with speed and efficiency, but after an initial brush with the Indigenous fighters at Fish Creek, Middleton became cautious and his tactics at the decisive battle of Batoche were ponderous. Nevertheless the campaign was successfully concluded and a grateful Canadian Parliament voted Middleton a monetary award, while the British government made him a KCMG and promoted him lieutenant-general.
He retired in 1890, but his plans to take over the presidency of a Canadian insurance company were spoiled by a minor scandal involving the misappropriation of furs during the North-West Resistance. In 1896 he was appointed keeper of the crown jewels, Tower of London.