In November 1796, Elmsley arrived at Niagara-on-the-Lake, soon after followed by his wife and father-in-law. Lieutenant-Governor John Graves Simcoe had left the province in July, choosing Peter Russell to act as administrator in his absence. Before he left Simcoe had ordered that the provincial capital was moved from Niagara to York, and Russell was busy organising the unwelcome upheaval. For legal reasons, Elmsley objected strongly to the move which brought him into conflict with Russell throughout 1797. In July, 1797, Parliament was held at York, but a compromise had been met with a bill passed to permit the courts to remain at Niagara-on-the-Lake for a further two years. Elmsley finally moved to York in the spring of 1798, building a large house that later became the Lieutenant-Governor's residence. The administrator and the chief justice continued to disagree about almost everything. Concerning land grants and tariffs with Lower Canada, Elmsley was greatly influenced by his friend Richard Cartwright, generally supporting the Loyalist and merchantpoints of view. In legal matters, he tried to adapt English law to Canadian circumstances but was consistently opposed by Allcock, who believed that there should be absolutely no tampering with English law, procedures, and precedents. Elmsley was one of the few university graduates in the province, and was much given to elegant phrases and Latin quotations, a habit that may not have endeared him to all his colleagues.
Lower Canada and death
When the Duke of Portland had appointed Elmsley to the Chief Justiceship of Upper Canada, he had also promised him promotion to the Chief Justiceship of Lower Canada as soon as the post became vacant. In 1800, fearing he would lose money with another move, Elmsley withdrew his claim. Despite his reluctance, he was appointed to the Lower Canadian post in 1802, following the resignation of William Osgoode. The salary was increased from £1,000 to £1,500 a year, and he was to be called to the Executive and Legislative Councils of Lower Canada with a 'seat next in Rank to the Lieutenant Governor.' He traveled to Montreal in February 1805 with plans to go to the United States after he had become seriously ill in November of the previous year. He died in Montreal on April 29, 1805.
Legacy
When the Fort York Government House was destroyed in the War of 1812 by an explosion from the British ammunition magazine, Chief Justice Elmsley's house was purchased on King Street and converted into the new Government House. Despite this it was still called Elmsley House for a long period.