Bernardi married in 1677, to a Dutch woman from a respectably wealthy family. He was recalled from Holland in 1687 by James II, but at the 1688 Glorious Revolution he remained loyal to James and was therefore compelled to again leave the country, being given command of a Jacobite division on his arrival in France. In the aftermath of the Battle of Killiecrankie he was sent to Scotland to assist in organising Jacobite resistance in the Highlands, but the ultimate failure of James's campaign in Ireland led him to attempt escape southwards towards London, near where he was arrested while attempting to board a ship for Holland.