Bea was a leading biblical scholar and ecumenist, who greatly influenced Christian-Jewish relations during the Second Vatican Council in Nostra aetate.

When Pius XII proposed appointing Bea to the College of Cardinals in 1946, Superior General Jean-Baptiste Janssens spoke out against it, as many felt the Holy See was showing preferential treatment to the Jesuits.

[3] Raised to the rank of cardinal before his episcopal consecration, Bea was created Cardinal-Deacon of S. Saba by Pope John XXIII in the consistory of 14 December 1959.

On 6 June 1960, he was appointed the first president of the newly formed Secretariat for Promoting Christian Unity, a Curial organisation charged with ecumenical affairs.

He received his consecration on the following 19 April from John XXIII himself, with Cardinals Giuseppe Pizzardo and Benedetto Aloisi Masella serving as co-consecrators, in the Lateran Basilica.

[9] After Alfredo Ottaviani, the heavily conservative head of the Holy Office, presented his draft of the schema on the sources of Divine Revelation, Bea claimed that it "would close the door to intellectual Europe and the outstretched hands of friendship in the old and new world".

They dealt with archaeological issues, exegesis of Old Testament texts, Mariology, papal encyclicals, the unity of Christians, anti-Semitism, Vatican II, relations to Protestantism and the eastern Orthodox Churches, and ecumenicism.