During the upheavals of the 1640s many churches were sacked and burned. A Cromwellian Inquisition of 1657 reported of the church at Tullylish that only the original walls remained. It was rebuilt as a Protestant church in 1698. The church in Donacloney was not destroyed in the 1641 rebellion although the Protestant clergyman resident there fled. The Church was eventually destroyed in 1689. In his Relatio Status, 1675, the Primate reported that there was a parish priest in each parish of the diocese of Dromore at that time. Curates, of course, could not be counted in view of the penal enactments then obtaining. Among priests of the diocese who were outlawed by a Williamite court held in Banbridge in 1691 was Fr. Edward Magennis from the Parish of Tullylish.

In 1704 there were 1,089 registered priests, of whom 189 were in Ulster. Normally they were not molested by government officials but in times of political crisis they might have been arrested on one pretext or another. On 11th July, 1704 a general session for registering was held in Downpatrick and there the Rev. Neile Burns, aged 54 years, who resided at Ballyvarley was registered as "Popish Priest of Seapatrick, Tullylish and Donacloney." He had been ordained by Daniel MacKey, R.C. Bishop of Down and Connor. In addition, no one could teach without a licence, Accordingly, Daniel McCoskran, "a Popist," was summoned to the Diocesan Court in 1739. This confirms what is stated in An abstract of the Returns of the Lord Bishop of Dromore, November 30th 1731, when His Lordship made his returns to the Government, stating that there was "one Popish school and two priests" in Tullylish Parish. It may be that the two priests were residing in the parish but that one was assigned to another parish.

We know from an advertisement in the Belfast Newsletter dated 6th. March 1770 that a Fr. Francis Polin ministered to the Catholics of Tullylish. Indeed it is quite possible that he celebrated at the Mass Rocks at Holy Mount, Clare, Knocknagore, Bleary or Ballynagarrick. The advertisement referred to above reads:
"Any person, who, in three Kalendar months from the date hereof, lodges in any of His Majesty's Gaols of this Kingdom. Francis Polin, otherwise McPolin (a Popish Priest of a profligate and abandoned character) charged before me upon oath with a Felony of a grievous Nature, Shall receive a Reward of Twenty Pounds to be paid by Rich'd Johnston Gilford, 3rd. March, 1770.”