Between April 28 and 30, American troops carried out many acts of plunder. Some of them set fire to the buildings of the Legislative Assembly, and Government House, home to the Lieutenant Governor of Upper Canada. It was alleged that the American troops had found a scalp there,^[36] though folklore had it that the "scalp" was actually the Speaker's wig. The Parliamentary mace of Upper Canada was taken back to Washington and was only returned in 1934 as a goodwill gesture by President Franklin Roosevelt.^[37] The Printing Office, used for publishing official documents as well as newspapers, was vandalized and the printing press was smashed. Other Americans looted empty houses on the pretext that their absent owners were militia who had not given their parole as required by the articles of capitulation. The homes of Canadians connected with the Natives, including that of James Givins, were also looted regardless of their owners' status.^[38] Before they departed from York, the Americans razed most of the structures in the fort, except the barracks.^[39]

During the looting, several officers under Chauncey's command took books from York's first subscription library. After finding out his officers were in possession of looted library books, Chauncey had the books packed in two crates, and returned them to York, during the second incursion in July. However, by the time the books arrived, the library had closed, and the books were auctioned off in 1822.^[40] Several looted items ended up in the possession of the locals. Sheaffe later alleged that local settlers had unlawfully acquired government-owned farming tools or other stores looted and discarded by the Americans, and demanded that they be handed back.^[41]

The looting of York occurred in spite of Pike's earlier orders that all civilian property be respected and that any soldier convicted of such transgressions would be executed.^[42] Dearborn similarly emphatically denied giving orders for any buildings to be destroyed and deplored the worst of the atrocities in his letters, but he was nonetheless unable or unwilling to rein in his soldiers. Dearborn himself was embarrassed by the looting, as it made a mockery of the terms of surrender he arranged. His soldiers' disregard for the terms he arranged, and local civil leaders' continued protest against them, made Dearborn eager to leave York as soon as all the captured stores were transported.^[43]