Many scholars contend that the “Glorious” Revolution of 1688 restrained governmental abuses in Britain by preventing the Crown from engaging in irresponsible behavior. However, the question of whether it imposed similar restraints on Parliament has received limited scrutiny. This oversight applies in particular to the religious sphere and outside of England. Rather than create the general conditions for liberty, we contend that the institutional legacy of the Revolution of 1688 was biased toward those in the winning coalition and that its positive effect on liberty is overstated. Analyzing the institutional legacy of the Glorious Revolution on religion in Scotland, we use narrative evidence and systematic evaluation of legislation to show that, rather than establishing the conditions for religious liberty in Britain, the revolution transferred power from one denomination to the other. The arbitrary religious repression symptomatic of the prerevolutionary Crown persisted because the religious liberties enshrined in the Revolution depended largely on whether a group was a member of its winning coalition. Whereas the Crown and the Episcopalians suppressed the Presbyterians prior to 1688, afterward an alliance between the Scottish Presbyterians and the English Parliament reinstated Presbyterianism as the established Scottish Church. This reversal allowed the Presbyterians to suppress the Episcopalians. Religious tolerance and attendant civil rights expanded only with secularization in the nineteenth century when the political representation of other denominations and religions increased and factionalism undercut Presbyterian monopoly.