The transformation of Irish towns in the early modern period (from bastions of English loyalism, to centers of Catholic resistance, to stridently Protestant colonial outposts) has received relatively little attention from historians. Instead, scholars have focused on the major land transfers of the seventeenth century, but the change in urban settlement patterns proved even more dramatic and was closely related to the positioning of civic communities in relation to the military struggles of the 1640s and 1650s. The central argument is that the Cromwellian conquest of Ireland marked a crucial and irrevocable transformation in both the possibilities of civic militarism and the nature of urban society and politics more generally. It demonstrates that during the 1640s, the citizens of Ireland’s major provincial cities participated in the troubles through strategic neutralism and the retention (or careful negotiation) of military force, acting with the fortunes of the citizenry in mind. This approach continued a tradition of relative civic autonomy, which was probably more embedded and accentuated in Ireland than either Scotland or England.