After emigrating to colonial America, he built Mount Pleasant in Philadelphia, Pennsylvania, in 1762.

[5] In 1762, he resigned his position on the Britannia, having been seriously injured on several occasions, including having an arm shot off twice.

He married for a second time in 1772, to Mary Ann MacNeal, with whom he had six more children: Charles, Amelia Sophia, Mary Ann, John Montgomery, Eliza Gates and Robert Hector.

In 1778, Macpherson leased Mount Pleasant to Spanish minister Juan de Miralles.

He is buried in the cemetery of Philadelphia's Old St Paul's Church.