At the disruption, Black attached himself to the Free Church, and in 1844 was appointed to the chair of Exegetical Theology in the New College, Edinburgh, from which he retired in 1856.

His great powers as a linguist and his very large and particular acquaintance with rabbinical literature caused him to be selected in 1839 by a committee of the General Assembly of the Church of Scotland, along with the Alexander Keith, St. Cyrus, Robert Murray McCheyne, Dundee, and Andrew Bonar, Collace, to go to the East to make inquiries as to the expediency of beginning a mission to the Jews.

After a good many difficulties and trials Black and his brethren returned to Scotland, and an interesting report of their mission was presented to the general assembly.

[3] On Black's return from the Holy Land, he found his most amiable and beloved wife in the last stage of an illness; he arrived only in time to see her expire.

Referring to the linguistic powers of Black and his colleague, John Duncan (Colloquia Peripatetica), Thomas Guthrie used to say that ‘they could speak their way to the wall of China;’ yet no corresponding products of their learning were given to the public.

His advanced years and reserved sensitive disposition hindered him from overcoming the difficulties in which he felt himself placed, as well as from forming new friendships to sustain him under them; and in 1856 he retired from his professorial charge.

But the heat of summer and the roughness of the mode of travel obliged Black and Keith to proceed homewards by the shortest route through Hungary, to the nearest continental port.