An active participant of the Second Vatican Council (1962–1965), Liénart was a leading liberal voice at the council and sat on its Board of Presidency. When the Roman Curia, composed predominantly of conservative prelates, issued a list of nominees for the members of the council's commissions, Liénart objected that nothing of the nominees' qualifications were included. Liénart, assisted by Cardinals Bernardus Johannes Alfrink and Giovanni Colombo, delivered one of the closing messages of the council on 8 December 1965. He was also one of the cardinal electors in the 1963 papal conclave, which selected Pope Paul VI.