The present church building was constructed in the early twentieth century under the direction of Mar Aloysius Pazheparambil and was elevated to the status of a Basilica by Pope Paul VI on 20 March 1974.

[5] The St. Mary's Cathedral Basilica in Ernakulam controversy reflects a deep-rooted conflict over liturgical practices, highlighting the Syro-Malabar Church's struggle between tradition and uniformity.

Adding to the origins of the dispute at St. Mary's Cathedral Basilica in Ernakulam, Archbishop Mar Antony Kariyil's tenure and resignation[6] further exemplify the complexity of the issue.

The Basilica witnessed the dispute take a violent turn[12][13] on 28 November 2022 when Archbishop Mar Andrews Thazhath, who was supposed to conduct the uniform mass as per prior assurance by then Archdiocese Metropolitan Vicar Mar Antony Kariyil (Kariyil had earlier agreed along with the priests[14] to move to uniform mode before December 25th, 2022 as per Pope Francis Directives communicated back in April 2022[15]), was blocked at the gates by the Vicars supporters (Athirupatha Samrakshana Samithi and Almaya Munnetta Samithi).

[16] On 17 August 2023, Archbishop Cyril Vasil, appointed by the Vatican to address the Ernakulam-Angamaly archdiocese dispute, ordered all parishes to follow the uniform mass format, with non-compliance risking excommunication.

On 18 August 2023, Almaya Munnetta Samithi claiming to represent all parishioners from the Ernakulam-Angamaly Archdiocese and its 328 dioceses petitioned President Droupadi Murmu,[18] seeking the deportation of Papal delegate Archbishop Cyril Vasil, citing interference in local church affairs.

The Pope's intervention highlights the urgency and importance of resolving internal conflicts within the Church, focusing on communal harmony and adherence to broader Catholic principles and prevent excommunication.