After doing ministry work across Texas, Cooper returned to SMU in 1965 as the Associate Chaplain where he stayed for seven years. During his time at SMU he was known for his activist work and for attempting to foster connections between religion and peacemaking. While at SMU, Cooper experienced the student senate’s invitation to Martin Luther King. Cooper recalls how there were hundreds of policemen at the event in anticipation of violence, however the gathering remained peaceful. At SMU Cooper worked with social activist groups such as the Un-committee and the Dallas chapter of Amnesty International on local issues of anti-apartheid and divestment.
As a result of his work at SMU, the Robert O. Cooper Peace and Justice Fellowship was established in his honor. Cooper still lives in Dallas with his wife.