He was ordained priest on 1 November 1900. Soon afterwards he appointed Vice-Rector of the Scots College. In 1907, he was made a privy Chamberlain. Mackintosh became rector of the College in 1913,[3] and was made a Domestic Prelate the following year.
According to Thomas Gerard Gallagher, by 1940, "Archbishop Mackintosh was a chronic invalid who was unable to get around his archdiocese or properly supervise its activities."[5] He died in office on 8 December 1943,[3] aged 67. He had been a priest for 43 years and a bishop for 21 years. He was the principal consecrator of Andrew Thomas McDonald, Archbishop of Saint Andrews and Edinburgh.[4]