He started as an assistant pastor in 1866. His first ministry began in 1868 at Innellan, on the Argyll coast between Dunoon and Toward. He stayed 18 years. His books on Aids to the Study of German Theology, Can the Old Faith live with the New?, The Growth of the Spirit of Christianity from the First Century to the Dawn of the Lutheran Era, established his reputation as a liberal and spiritually minded theologian; and Queen Victoria invited him to preach at Balmoral. She had his sermon on Job published. In 1886, he moved to Edinburgh, where he became minister of St. Bernard's Parish Church inStockbridge for 13 years. Here his chief work as a preacher was done. In 1879, he declined an invitation to the pastorate of Crown Court, London, in succession to Dr. John Gumming. In 1881 he was chosen as Baird lecturer, and took for his subject Natural Elements of Revealed Theology, and in 1882 he was the St Giles lecturer, his subject being Confucianism. In 1890 he was elected a fellow of the Royal Society of Edinburgh, the University of Aberdeen gave him its honorary LL.D., and in 1899 he was appointed Gifford lecturer by that university, but declined on grounds of health. In the same year he severed his active connection with St. Bernard's.
Published works
One of his hymns, "O Love That Wilt Not Let Me Go," has passed into the popular hymnology of the Christian Church. Matheson himself wrote of the composition: "O Love That Wilt Not Let Me Go" was written on the evening of Matheson’s sister’s marriage. Years before, he had been engaged, until his fiancée learned that he was going blind—that there was nothing the doctors could do—and she told him that she could not go through life with a blind man. He went blind while studying for the ministry, and his sister had been the one to care for him through the years, but now she was gone. He was now 40, and his sister’s marriage brought a fresh reminder of his own heartbreak. It was in the midst of this circumstance and intense sadness that the Lord gave Matheson this hymn, which he said was written in five minutes. Matheson published only one volume of verse, Sacred Songs. All of which he commented 'I simply followed the impression of the moment' His exegesis owes its interest to his subjective resources rather than to breadth of learning; his power lay in spiritual vision rather than balanced judgment, and in the vivid apprehension of the factors which make the Christian personality, rather than in constructive doctrinal statement. His other writings include :