Following the accession of James VII in 1685, Bruce gradually fell from favour, and was distrusted by the new regime. After the Revolution of 1688, and the accession of William of Orange as King, he was once again at odds with his Protestant rulers, and he refused to take up his seat in Parliament. As a staunch Episcopalian, Bruce was considered a potential Jacobite threat. In 1693 he was briefly imprisoned in Stirling Castle for refusing to appear before the Privy Council. He was incarcerated again at Stirling in 1694, and from 1696 in Edinburgh Castle. Bruce was expelled from parliament in 1702, his seat passing to his son John Bruce. Despite these imprisonments, he continued his architectural work, indeed the 1690s and 1700s were his most prolific years. Bruce was imprisoned at Edinburgh Castle again in 1708 and was only released a short time before his death, at the beginning of 1710.