Oliver Cromwell led his New Model Army in the conquest of Ireland, which lasted until 1653, though the Cromwellian regime remained in force until the restoration of Charles II in 1660. Cromwell had several reasons for invading Ireland. After the 1641 rebellion against Protestant landowners, England had lost control over two thirds of Ireland, which were being governed instead by the Irish Catholic Confederation (also known as the Confederacy of Kilkenny). An alliance between the Irish Catholic Confederacy and the English Royalists was a huge cause for concern for Oliver Cromwell's new regime. Among the Parliamentarians there was a desire to avenge the Protestants affected by the 1641 uprising. As Puritans they considered Catholics heretics, worth crusading against. Finally, but importantly, there was also the financial incentive to pay off Parliament's creditors with land conficated from Catholic rebels.
In Stradbally, the church would have closed under the Cromwellian regime. It was possibly reopened during the reign of the Catholic James II, but was certainly ruined by the 18th century, where graves dating to early on in the 18th century began to be dug inside the church.