He attended the Second Vatican Council (1962–1965), the First Ordinary Assembly of the Synod of Bishops, Vatican City (1967), the First Extraordinary Assembly of the Synod of Bishops, Vatican City (1969) and the Second Ordinary Assembly of the Synod of Bishops, Vatican City (1971). He was elected a member of the Council of the General Secretariat of the Synod of Bishops (1971).
Cordeiro was honoured by the Christ the King Seminary in Karachi that has hosted the Cardinal Cordeiro Cricket tournament to promote religious vocations since 2008.[11]
On 6 May 2011, The Old Patricians (former students of St Patrick's school) presented the Joseph Cardinal Cordeiro Gold Medal to the top student from the Cambridge A level section at the closing ceremony of the 150th anniversary of the school.[12]
In 2012, Cardinal Cordeiro High School was named in his honor. The school is located in the Good Shepherd Parish in Korangi Town, Karachi.[13]
His alma mater, St. Patrick's High School named the Cardinal Cordeiro Silver Jubilee Auditorium in his honor.