He reluctantly joined the rebellion of 1837 and protected the loyalist prisoners at Montgomery's Tavern from abuse. However, despite this, the governor Sir Francis Bond Head ordered his farm burned. Gibson fled to Lockport, New York, where he was employed as an engineer for the Erie Canal. In 1848, having been pardoned in 1843, he returned to his farm and was hired as a provincial land surveyor. In 1853, he was given the post of inspector of crown lands agencies and superintendent of colonization roads in Canada West. He also supervised the surveying of roads in the Algoma District from 1861 to 1862. For a time, he also operated a large sawmill in the Parry Sound region, which was later taken over by William Beatty.