In the Resolutioner versus Protester schism in the Church of Scotland during the Cromwellian invasion of Scotland, Baillie sided with the Resolutioners. His ecclesiology saw the church as an "ecclesia mixta", comprising both reprobate and elect. He rejected the Protestors' more exclusive vision of a church of visible saints in which membership (and by extension the ability to hold church office) should be restricted to godly "true" believers. Baillie's concern was to maintain church unity and combat the threat posed by sectarians.