In 1789, Macaulay's former commanding officer, John Graves Simcoe, recommended him to the post of surgeon to the New South Wales Regiment, but he did not go to Australia.

When Simcoe was appointed Lieutenant Governor of Upper Canada in 1791, he began organizing his staff before he set sail and he chose Macaulay to be his chief surgeon in the new Canadian colony.

Macaulay acquired several large parcels of land there due to his military service, and helped by his close friendship with the Lieutenant-Governor.

In 1808, he lost the post to William Somerville, the Deputy Inspector of Hospitals on the staff of Sir James Henry Craig, Governor-General of the Canadas.

In 1813, he served with Lieutenant-General Sir George Prévost at the attack on Sackets Harbor, New York, and, following his appointment that July as Deputy Inspector of Hospitals, was with Major-General Francis de Rottenburg on the Niagara Peninsula.

With James Baby, Peter Robinson (1785–1838) and others, he was appointed to a commission formed in 1819 to deal with estates forfeited during the War of 1812, and he joined with other members of York’s élite, including William Allan, Thomas Gibbs Ridout and William Warren Baldwin in promoting the bank which was to be chartered as the Bank of Upper Canada.

The York Observer reported at his death, It becomes our painful duty to communicate to our readers the decease of Dr Macaulay of this town.

He was ever ready to wait upon and relieve the forlorn stranger not only with his medicine, but with his purse; and it is to be hoped that those gentlemen who are left behind will endeavour to imitate his unbounded liberality.

She was the daughter of Naval Lieutenant Samuel Hayter (1737–1800) of Wareham Priory, and formerly of East Creech Manor, Isle of Purbeck, Dorset; a grandson of Captain Seth Jermy.