On May 18, 1940, Msgr. Joseph Charbonneau was appointed Coadjutor Archbishop of Montreal to assist and eventually succeed Msgr. Georges Gauthier who was alone, in poor health, and who died on August 31. That same day, at the age of 48, Archbishop Charbonneau became titular Archbishop of Montreal.

Though little known here in Montreal, the man impressed many. Large in stature, noble in habit with a broad forehead and graying hair, he was the very essence of distinction. His delicate but confident voice forced people to listen and his often innovative views were surprising and thought-provoking.

The first act of Msgr. Charbonneau was the opening of the School of Social Work at the Université de Montréal in October 1940; a school long desired by his predecessor. It can be viewed as an indication of the social concerns of the new Archbishop.

On June 29, 1941, he published his Letter on Catholic Action (64 pages), a major document of his episcopate in which he reviewed the lived experiences, the structures, the projects, the directions to be taken for an apostolic movement which developed within the Church of Quebec since the mid-1930s and which was called to grow widely within it. The Archbishop wrote of the confidence he placed in the younger generations and the place that lay Christians must take in all sectors of human activity.

On August 15, 1941, he conferred episcopal ordination on two vicars general, whom he made his auxiliaries: Msgr. Joseph-Conrad Chaumont and Msgr. Lawrence Patrick Whelan. He became the first English-speaking bishop to be a member of the diocesan curia of Montreal. Msgr. Charbonneau's desire to recognize the place and role of the English-speaking community within the Church of Montreal was an audacious move; one which some French-speaking Catholics considered questionable. Msgr. Charbonneau was not afraid to innovate.

In the fall of 1941, the Archbishop, with the help of Mr. Georges Perras, p.s.s., set up the École normale secondaire to train teachers for classical teaching. Its focus was with an educational concern and a search for competence in teachers of this level.

In a similar manner, Msgr. Charbonneau attended the first Congrès de l’enseignement secondaire (classique) in the summer of 1942. In an address to the participants, directors, and professors of all the classical colleges in Quebec, he had the boldness to express his regret to see the entrance to universities restricted only to those with a bachelor's degree in arts; that there were so many other young people to bring to the university level. In his eyes, there was a huge loss of talent in Quebec. That was long before the rapport Parent.

On February 2, 1943, the Archbishop founded the l’Oeuvre des vocations, another initiative concerning the preferment of priests, which he entrusted to Mr. Arthur Delorme, p.s.s. l’Oeuvre des vocations proves to be a necessity more than ever nowadays.

Aware of the role and importance of the family in the Church and in society, and to mark the fifth anniversary of the one hundred and five J.O.C. marriages, he appointed Father Albert Sanschagrin O.M.I. in 1944 as chaplain of the Marriage Preparation Service. A member of the J.O.C., he responded to a real need and obtained remarkable success: in three years, 3,000 couples received Christian marriage training there. The formula created here in Montreal was implemented in several countries.

In 1945, the Family Education Service appeared, a diocesan coordinating body, in which the Franciscan Fathers became intensely involved in studying the various problems of the family and supporting it.

Following in the footsteps of his predecessors at the headquarters in Montreal and as Chancellor of the Université de Montréal, Msgr. Charbonneau closely followed its development. In 1947, he launched an $11 million fundraising campaign in his diocese. This was the first major undertaking for the newly established university since its establishment in 1942 on the slope of Mount Royal.

It is also worth emphasizing his concern for poor children who died prematurely, his concern about the problem of housing in his diocese, his concern for how to respond to the spiritual needs of a growing population through the foundation of parishes (25 during his episcopate), the welcome he gave new religious communities, and his fundamental predilection for the small and the poor.

Nothing illustrates this concern better than his attitude during the famous asbestos strike at the Asbestos and Thetford Mines in 1949. His actions were the most significant in popular opinion during his episcopate. To give a voice to the declaration of the Sauvons les travailleurs de l'amiante on May 1, 1949, he publicly and firmly took a position that very day at Notre-Dame Church in Montreal in favour of the striking asbestos workers. Hammering his words, he said in particular:

“The working class is the victim of a conspiracy that wants to crush it, and when there is a conspiracy to crush the working class, it is the duty of the Church to intervene. Our heart is close to this working class and we designate this collection to prevent small children from suffering from hunger.”

This intervention by the Archbishop of Montreal had profound and numerous echoes. Collections were held throughout the province and his stance was no stranger to the resolution of the conflict.