On 5 November 1981, Pope John Paul II appointed Micallef as the third Apostolic Vicar of Kuwait. He was consecrated by the Pope himself on the feast of the Epiphany 1982. On 15 January of the same year, he was officially installed as the Apostolic Vicar of Kuwait and Titular Bishop of Tinis in Proconsulari. Micallef remained in Kuwait City during the 1990 Iraqi invasion, one of the few Westerners to do so.