Returning to Connor diocese and the Belfast area, Bishop Harper moved to be incumbent of Malone from 1986-2002.

From 1999-2002 he was also Archdeacon of Connor and Precentor of St Anne's Cathedral, Belfast.

Bishop Harper's long-standing interest in archaeology and history led him to be appointed Chairman of the Historic Monuments Council for Northern Ireland from 1986-1995. In 1996 he was appointed an OBE for Services to Conservation in Northern Ireland.

Bishop Harper is perceived to be liberal on a number of social issues. Speaking on BBC Radio Ulster in September 2003, Bishop Harper affirmed permanent homosexual relationships: "if a relationship between homosexual males is creative of love as well as being permanent and lifelong I don't think that I am able to say that it is intrinsically disordered. What I am very much concerned about is the problem of promiscuity which is a totally different issue. I'm not entering now into the question of whether or not a homosexual lifestyle as we see it is intrinsically more promiscuous than what we call a straight lifestyle. But I am concerned about faithfulness."

This is similar to what he said to his diocesan synod in 2003 about cohabiting heterosexual couples: "That form of cohabitation in which couples commit themselves to each other in a loving, consenting, exclusive, permanent relationship is a form of commitment less complete than marriage, and therefore not the same as marriage, but is, nevertheless, a state of life which may be chosen in good conscience and is deserving of respect."

While affirming such extra-marital partnerships, he clarified to a diocesan conference in 2003 that he "could not and would not ordain to the diaconate or the priesthood any person whom I knew to be engaged in an active homosexual relationship. I believe that such an action would be in conflict with the mind and the accepted practice of the Church of Ireland. I also believe that such a deacon or priest living openly in an active relationship might well be vulnerable to an action brought in a church court for the offence of 'conduct unbecoming'."

More recently he has written to his clergy on the 'blessing' of civil partnerships, advising against using such liturgies on legal and constitutional, rather than scriptural or moral grounds: "The Church of Ireland has not considered, provided or authorised any order of service for the Blessing of a Registered Civil partnership. I consider that the devising of such a liturgy by any member of the clergy at this time . . .would be likely to constitute a variation 'of substantial importance' in any form of service prescribed in the Book of Common Prayer or elsewhere. It might also be deemed or interpreted by some to be indicative of a 'departure from the doctrine of the Church.' "

Just before Christmas 2006, he represented the Church of Ireland at the Colloquium on Same Sex Relationships for churches of the Porvoo Communion which examined, amongst other things, the order for blessing homosexual partnerships recently adopted by the Church of Sweden.

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