In 1960 he was sent to the College of the Resurrection and St Peter in Rosettenville as principal of the seminary in which the CR fathers trained almost all black priests for the northern dioceses of the Anglican Church of Southern Africa for most of the 20th century.
[2][3] St Peter's College was later forced to close by the apartheid government because it was in a white group area but taught black students.
Stubbs successfully argued for its relocation to Alice, Eastern Cape as part of the multi-denominational Federal Theological Seminary of Southern Africa.
[2] According to Barney Pityana he "went out of his way", travelling across the country to visit past and present activists such as Biko, Mamphela Ramphele and Robert Sobukwe.
At a crucial period in South Africa’s history, he deeply influenced a whole group of black ordinands, including Desmond Tutu.