The English protectorate began in 1653 with a conspiracy of politicians, army officers, and religious leaders against a theocratic strain of puritanism. Among the plotters was John Owen (1616–83), the leading religious authority of the Interregnum, vice-chancellor of Oxford University, and the ‘Cajoler of Cromwell’. When amid a military and republican coup parliament was dissolved and Richard Cromwell removed in 1659, Owen was again at the heart of events. But the narrative became that this time he had used his influence to oppose the Cromwells. As minister of a congregation at the centre of the nation’s halls of power composed of the military and political elite, Owen became seen as Richard Cromwell’s ‘instrument of ruine’. This article challenges that narrative and its appearance in histories of early 1659 and of Owen’s biography by utilizing new sources and re-evaluating known evidence within the broader context of religious and political divisions at the end of the protectorate. Owen supported whatever political form could best preserve the long-term safety of the English commonwealth and godly rule against the Stuarts. Yet Owen’s legacy became contested among the godly after the Restoration, as the agent of the protectorate’s fall and the failure of puritan politics.