In 1781, Munro was stationed in Montreal, in charge of the housing and care of the many Loyalists refugees who ended up there, before being placed in command of the garrison at Coteau-du-Lac, Quebec. In 1783, at Sir Frederick Haldimand's request, he undertook a tour of exploration from Quebec City to Halifax via the Témiscouata route on behalf of a group of Loyalists who had obtained land in Nova Scotia. Munro reported on the route and on the suitability of lands in Nova Scotia and present-day New Brunswick.
