In 1966, he joined the Commonwealth Secretariat as Assistant Director of International Affairs. In 1968-69 there was a campaign by the Nigerian military government for the recall of Anyaoku; which said he was not a suitable Nigerian nominee, and they were anxious about his loyalty to the country of his birth. But Emeka had resigned from the Nigerian Foreign Service and Arnold had no difficulty in turning aside the demand.
In 1977, the Commonwealth governments elected him as Deputy Secretary-General.
In 1983, Nigeria's civilian government appointed Anyaoku to become Nigeria's Foreign Minister. After the overthrow of the Government by the military later that year, he returned to his position as Deputy Secretary-General with the support of the new government in Nigeria and the endorsement of all Commonwealth Governments.
At the Commonwealth Heads of Government meeting at Kuala Lumpur in 1989, Anyaoku was elected the third Commonwealth Secretary-General. He was re-elected at the 1993 Limassol CHOGM for a second five-year term, beginning in July 1995.
Anyaoku is currently President of the World Wide Fund for Nature.