He returned to South Africa in 1935 and in 1936 was appointed Lecturer in Social Anthropology and Native Law and Administration at University of Fort Hare.

After Davidson Don Tengo Jabavu’s retirement in 1944, Matthews was promoted to Professor and became head of Fort Hare’s Department of African Studies.

In 1943, he was elected to the National Executive Committee and at the same time he became a member of the Native Representative Council, a purely advisory body that has been condemned as a “toy telephone” and which Z.K.

In June 1952, on the eve of the Defiance Campaign, he left South Africa, and took up a position as visiting professor at New York's Union Theological Seminary.

He returned home in May 1953, and although not present at the Congress of the People in 1955, he assisted Lionel "Rusty" Bernstein in drawing up the Freedom Charter that was adopted there.

On his release from the trial in late 1958, he returned to Fort Hare, but resigned his post in protest against the passing of legislation that reduced the university to an ethnic college for the Xhosa community only.