He was ordained in Clarendon Street Chapel, Dublin, by Bishop John Francis Willian Whelan OCD Roman Catholic Archdiocese of Bombay on 18 September 1852 and was given his first appointment as Curate of Ballymena on 18 November 1852.
He was sent on a temporary mission, as locum tenens to Glenravel, while the priest there was engaged in building St Patrick's Church in the Braid, where he officiated from December 1853 until March 1854.
At a meeting of the parish priests held in the chapel of St. Malachy's College immediately after Bishop Dorrian's funeral, McAlister was elected Vicar Capitular of Down and Connor.
When Dr. McAlister, on 9 July 1886, made his first episcopal visitation of the parish of Ramoan, a deputation of the parishioners waited on him at the Parochial House for the purpose of reading to him an address and presenting him with a pectoral Cross and Chain.
The following is a copy of the address : – "My Lord, – It is with sentiments of the deepest filial affection that we, your own beloved parishioners, desire to bid your lordship a hearty welcome to-day, and to express our thanks that Almighty God, although depriving us of a loving pastor, has been pleased to place the mitre of this illustrious diocese on the head of one so learned so patriotic, and so holy".
"My Lord, your life for the past 23 years has been entirely devoted to our service, you have raised in our midst a magnificent Church, of which we are justly proud, and which, together with the Parochial House and Schools, you have given us, shall long remain a monument of your energy and zeal.
But the hand of God has raised you to a more exalted position and we sincerely pray that He may grant you long years of health and happiness to rule your faithful people".
"We beg you will he pleased to accept, as a slight token of our deep love for you, the accompanying Pectoral Cross and Chain, and that you will ever regard us as your own especial care, and Ballycastle as your home".
I will commend you to the prayers of Saint Patrick and Brigid, and ask those Holy Patrons of our parish and our country to obtain for you the grace to be always true to faith and fatherland To-day I wish to bring back to your recollection, that when I undertook to build your church and its altar, the primary object I had in view was to erect a becoming sanctuary, where our Divine Saviour, in the Sacrament of His love, might deign to dwell in your midst, and to bless you.
And, as in my present position, I need much the aid of your holy prayers, I ask you, my dear friends, when you pay your visits to our Lord on the altar, to commend me to the mercy of His Sacred Heart".
McAlister was Bishop of Down and Connor for only nine years, but during that episcopate he had to cope with the worst riots of the 19th century in Belfast, triggered by the home rule bill of 1886.