For a year and a half, from the spring of 1672 to the autumn of 1673, Stubbe was attached to the court. He wrote his two major propaganda pieces in ‘the Paper Office at Whitehall,’ and was paid £200 for the job. But Stubbe's career as a court pamphleteer was short-lived. By October 1673 he was recognized as one of the leading propagandists for the ‘country’ opposition that was just then emerging.

Churchmen had remained suspicious of Stubbe, while he wrote for the court. His vigorous defense of the Indulgence did nothing to win them over. During 1673 William Sancroft, Dean of St Paul's, received reports of Stubbe's activities, and in one of these he was clearly associated with the Erastian, tolerationist opinion at court, so despised by the clerical hierarchy.