During the Confederate Wars in Ireland (1641–1653), her husband led and financed one of the five militia companies of Clare which raided tower houses of English settlers planted in the area during the preceding century. O'Brien is reported to have ridden with her husband during some raids. In depositions relating to the Irish Rebellion of 1641, a man named Gregory Hickman stated that: "Conor O’Brien, gentleman, in a most rebellious manner seized upon the deponent’s corn"; and, later, "Conor O’Brien, of Lemaneagh, accompanied by Mary Brien [and others] with force of arms came to the deponent's house and took away fourteen English swine and a parcel of household stuff; also 400 sheep". Some of those raided by O'Brien reputedly perpetuated rumours that she was a witch.