The yeomanry shot the parish priest in bed and Murray, to escape a similar fate, fled to the city where for two years he served as curate at St. Andrew's Chapel on Hawkins Street.

He was then assigned to the Chapel of St. Mary in Upper Liffey Street where Archbishop John Troy was the Parish Priest.

[3] Murray was an uncompromising opponent of a proposal granting the British government a "veto" over Catholic ecclesiastical appointments in Ireland, and in 1814 and 1815, made two separate trips to Rome concerning the controversy.

Murray persuaded Edmund Rice to send members of the Christian Brothers to Dublin to start a school for boys.

Among his last priestly functions was a funeral service for Richard Lalor Sheil who had died in Italy, and whose body had been brought back to Ireland for burial.

He was interred in the pro-cathedral, Dublin, where a marble statue of him has been erected in connection with a monument to his memory, executed by James Farrell, president of the Royal Hibernian Academy of Fine Arts.

[10] He had hesitation, however, in accepting the adverse decision of Rome, and was present at the Synod of Thurles where the Queen's Colleges were formally condemned.