His vocal support of Palestinian rights during the 1967 war led to his isolation within the academic community, causing him to leave Cornell. From 1968 to 1972, he worked as a fellow at the University of Chicago. During this time, Ahmad became a strong activist against the Vietnam War, which lead to his being charged as part of the Harrisburg Seven in January 1971. After the trial Ahmad was acquitted of all charges in 1972. He moved to Amsterdam in 1973. In 1974, he founded and directed the Transnational Institute, until 1975. In 1982, he moved back to the United States and joined the Hampshire College as a tenured professor and taught there until becoming Professor Emeritus in 1997.