After defeating the Royalist Glencairn's Rising in 1654, the new administration decided to draw a line under the civil wars and adopted a number of conciliatory measures.

He was known as an opponent of Presbyterian radicals and in 1675, his uncle by marriage, the Duke of Lauderdale, named him Lord Justice General, replacing the Marquess of Atholl.

He helped enforce increasingly harsh policies, including the death penalty for preaching at services held outside the approved church, or Conventicles, and was made a Commissioner of the Treasury in 1678.

However, measures for Catholic relief undercut the moderate Presbyterians and Episcopalians who then controlled the Church of Scotland and formed James' main support base.

Their opposition forced him to rely on an ever smaller circle of loyalists; in 1686, Moray was appointed Lord High Commissioner to the Parliament of Scotland, charged with ensuring repeal of the 1681 Test Act.