This article examines the Church of Ireland’s relationship with Scots Presbyterians after the Restoration, focusing on the churchmen’s regular complaints against the ‘disorderly’ practices of the Presbyterian communities in Ireland. The established church leaders spoke of the threat of political and social disorder from the Presbyterians, and they repeatedly targeted the spontaneous ex tempore prayer and preaching practised by Scottish ministers in order to illustrate their concerns. This article uncovers the theological roots of these apparently civic complaints to explain their ubiquity and vehemence. It argues that the churchmen feared that such uncontrolled, unscripted prayer could lead to blasphemy and provoke the wrath of God on the nation, thereby triggering war and unrest such as they had experienced in the preceding decades. In their view, there was little difference between holding to an improperly ordered church hierarchy and worship practice, and forcing this disorder on the state. By illustrating the links between theology, ecclesiology and the potential for political sedition as they were understood by Restoration churchmen, this article demonstrates the importance of theological nuance for clarifying the complex relationship between Ireland’s two largest Protestant denominations in the seventeenth century.