He was principally responsible for changing a small mission with several priests in four parishes into a large diocese with over 40,000 congregants and was the single most influential Irish immigrant to come to the Colony of Newfoundland in the 19th century.

His experience in helping to rebuild the Franciscan chapel there marked him at an early age as a "builder", and stood him in good stead for his later work in Newfoundland.

[citation needed] In 1823, at the invitation of Thomas Scallan, O.S.F., the Vicar Apostolic for Newfoundland, and the Benevolent Irish Society, Fleming was recruited to come and serve as a priest in the colony.

[citation needed] Despite their very different perspectives on many matters, Fleming was promoted by Scallan as his successor, and he was appointed coadjutor bishop of the vicariate by Pope Gregory XVI on 10 July 1829, with the titular see of Carpasia.

[citation needed] Soon after Fleming was consecrated as a bishop by Scallan in the Chapel in St. John's on 28 October 1829, he implemented his Ultramontanist ideology, taking over control of the existing Catholic institution the Orphan Asylum from its lay administrators, the members of the Benevolent Irish Society.

He took pains to visit outport Newfoundland, and during the winter of 1835 lived in a fishing room at Petty Harbour, administering smallpox vaccine to the whole community of Catholics and Anglicans, and remaining in quarantine with them when no physician or other clergyman would go there.

Whether in church administration, education or political activities, Fleming's bold actions and attitude marked a significant departure for the Catholic clergy in the Newfoundland colony.

He saw himself as the leader of the Irish community and was not shy about taking on the local British establishment, much as his friend and countryman Daniel O'Connell was doing at home, especially since he felt threatened by the Church of England's attempts to counteract growing Catholic influence.

The threat of violence was such that Bishop Fleming intervened, and persuaded them to adopt a common flag, on which the pink and green would be separated by a white stripe to symbolize peace.

Fleming's greatest domestic projects, the ones for which he became best remembered, were the recruiting of two orders of Irish religious women to work as teachers, and the construction of a new cathedral for St. John's.