It was originally created on 12 June 1514 by the papal bull Pro excellenti præeminentia from Pope Leo X, following the elevation of Funchal from a village to the status of city, by King Manuel I of Portugal (Royal Decree of 21 August 1508).

For twenty-two years it was, geographically, the largest metropolitan ecclesiastical province in the world,[3] having as suffragan dioceses: Azores, Brazil, Africa[4] and Goa.

In 1551 Pope Julius III revoked the situation by passing Funchal to the simple suffrage bishopric of the Archdiocese of Lisbon, as it remains today.

Although local authorities, at the time, had sought to isolate the sick in order to control the plague outbreak, the efforts made seemed to be vain.

Gaspar Frutuoso, in his book Saudades da Terra accounts that "the city's Chapter and Senate resolved to choose by random ballot a patron saint among the Apostles... After having prayed before God, a boy named John picked a note, where the name of James Minor was written, and they soon rejoiced all over the city.

Mannerist sobriety is clearly visible in the northern arch or in the Chapel of Saint Louis of Toulosa, which has an inscription on the façade with the name of its founder, D. Luís de Figueiredo Lemos and dated 1600.

[10][11] With the visit of the Ajuda Palace's Curator Manuel Cayola Zagallo, the diocese became more and more aware of the importance of the Flemish Art collection it owned and that was spread throughout the churches and chapels of its territory.

After important conservation and restoration work by Fernando Mardel, the paintings were exhibited in Lisbon at the National Museum of Ancient Art in 1949.

To this set were added other works, especially of Goldsmithing, Ecclesiastic Garments and Sculpture, mostly from Portuguese workshops, which were, in many cases out of worship and in poor condition, in many churches of the diocese, and which became part of the Museum's collections.

[10][12] Together with the Regional Government of Madeira the diocese promotes, by allowing its churches to act as concert venues,[13] for the island's Organ Festival.