Upon his return to Canada, he was named professor of dogmatic theology and of ecclesiastical history at the Seminary of Quebec in July 1868, remaining in those posts until 1884. He obtained the agrégation, a competitive examination for positions on the teaching staff of lyceums and universities, in 1869. From October 1870 to 1875, Bégin was Professor of ReligiousCulture at his alma mater of the Université Laval. He held an array of administrative posts from 1876 to 1883, such as director of the boarding school, of students, of seminarians, and prefect of studies. Bégin took several months for rest and recuperation from the end of 1883 to the beginning of 1884, and acted as the private secretary to Cardinal Elzéar-Alexandre Taschereau on his tour in Europe from April to December 1884. He served as Principal of the Normal School of Laval from January 1885 to October 1888 as well.
He was promoted to Titular Archbishop of Cyrene on December 18, 1891 and named Coadjutor Archbishop of Quebec on December 22. Illness forced Cardinal Taschereau to delegate his workload to Bégin, who was made Apostolic Administrator of Quebec on September 3, 1894. He eventually succeeded the late Cardinal as Archbishop of Quebec on April 12, 1898. Archbishop Bégin was appointed an Assistant at the Pontifical Throne on April 22, and participated in the First Plenary Council of Canada in June 1909.
Stricken by uremia followed by paralysis[4] on June 12, 1925, he died shortly thereafter at the age of 85. His body lay in state in the chapel of his residence, guarded by a detachment of the Papal Zouaves.[2] He was buried in the crypt of the Cathedral-Basilica of Quebec on July 25.
