 Clifford served on the Emigrant Commission of the Bishops' Conference and, in 1987 helped to set up the Chaplaincy Scheme to the young emigrants in the USA..

On 24 March 2010 it was announced by the Holy See that John Magee had formally resigned from his duties as Bishop of Cloyne and was now bishop emeritus and that Clifford, already apostolic administrator there, will remain as such until the appointment of a full-time successor to the Cloyne diocese.In July 2011 Clifford wrote to the lay faithful of Cloyne and apologised for the poor way in which complaints had been handled by diocesan officials in the Diocese of Cloyne

Clifford served as Apostolic Administrator to the Diocese of Cloyne until the new bishop, William Crean was ordained and installed on 27 January 2013.In October 2010, Archbishop Michael Neary of Tuam, along with Cardinal Seán Brady, Archbishops Diarmuid Martin of Dublin and Dermot Clifford of Cashel and Emly met for high-level talks with heads of Vatican congregations over the apostolic visitation of Irish dioceses in the wake of the Murphy and Ryan reports.