[4] In 1250, Manfred of Sicily found it necessary to rebuild Siponto in a new nearby location, only four miles away, which he named Manfredonia.

[5] Among the archbishops were Matteo Orsini (1327), later cardinal; Cardinal Bessarione (1447), administrator; Niccolò Perotti (1458), a Greek scholar and theologian; Giovanni del Monte (1512), later Pope Julius III; Domenico Ginnasio (1586), who suppressed the use of the Greek Rite at the high altar of the cathedral of Sipontum, a custom which had been observed until his time; Antonio Marcello (1643), who founded the seminary and restored the cathedral destroyed by the Ottoman Turks in 1620; Cardinal Vincenzo Orsini (1675), who became Benedict XIII (1724–1730).

In 1627, a major earthquake in the region of Gargano caused a tsunami which inundated the coastline of Apulia, including the city of Manfredonia.

[8] The right of the king to nominate the candidate for a vacant bishopric was recognized, as in the Concordat of 1741, subject to papal confirmation (preconisation).

[9] On 27 June 1818, Pius VII issued the bull De Ulteriore, in which he reestablished the metropolitan archbishopric of Siponto (Manfredonia), but with no suffragan dioceses at all.

[10] On 30 April 1979, Pope John Paul II undertook the reorganization of the dioceses of the region of Apulia.

Based on the revisions, a set of Normae was issued on 15 November 1984, which was accompanied in the next year, on 3 June 1985, by enabling legislation.

According to the agreement, the practice of having one bishop govern two separate dioceses at the same time, aeque personaliter, was abolished.

By order of Pope John Paul II, it became Archdiocese of Manfredonia–Vieste–San Giovanni Rotondo / Sipontina-Vestana-Sancti Ioannis Rotundi (Latin).

The stated reason for the change was the desire to honor S. Pius of Pietrelcina, who had founded a hospital for the suffering (Casa Sollievo della Sofferenza) in the city of San Giovanni Rotundo.