He was first brought into government in 1676 by the Duke of Lauderdale, his relative by marriage; between 1681 and 1686, he played a prominent role in the suppression of Presbyterian radicals, known as "the Killing Time".

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.