It was excised from the Archdiocese of Manila on December 11, 1961, by Pope John XXIII and was officially established on March 11, 1962, upon the installation of Manuel P. del Rosario, then-Bishop of Calbayog, by Salvatore Siino, the papal nuncio, as the first bishop of the diocese.

On the occasion of the diocese's 25th anniversary, the first synod was held in June to July 1987, with the theme, "Prepare for the Lord a Perfect People" (Lk.

Despite his short tenure, much of his pastoral work in the Bulacan local church involved fulfilling most of the plans Almario left of, part of which is the elevation of the Malolos Cathedral into a minor basilica.

In December 1999, at the inauguration of the Great Jubilee Year 2000, the Diocese of Malolos witnessed the elevation of its cathedral as minor basilica granted by Pope John Paul II together with the episcopal coronation of its patroness, La Virgen Inmaculada Concepcion de Malolos.

During the journey of the Diocese, the Jubilee Cross and the replica image of La Virgen Inmaculada Concepcion de Malolos joined the community in its journey towards the different religious, social, cultural and beneficial gatherings held during the five-year preparation, which was a remarkable opportunity for people to renew their faith in the Lord.

The diocese fulfilled four jubilee projects: the Jubilee Shelter Program in Plaridel, Bulacan under the Commission on Social Action, for those who need homes due to the devastation of Typhoon Ondoy; the Diocesan Pastoral Center in Malolos City under the Diocesan Curia; the Diocesan Formation Center in Guiguinto, Bulacan, under the Commission on Formation for different seminars and events of the Diocese and the Bahay Pastoral in San Ildefonso, Bulacan, a home for retired and sickly priests.

Villarojo once served as personal secretary to the late Cardinal Ricardo Vidal who was former Coadjutor Bishop of Malolos.

In February 2020, Pope Francis granted the canonical coronation of the image of La Purisima Concepcion in Santa Maria, Bulacan and in September 2021, he also granted the diocese a new minor basilica, the Minor Basilica of La Purisima Concepcion, Santa Maria, where the image is enshrined.

On March 11, 2022, the diocese celebrated its 60th anniversary with a Mass presided by the Apostolic Nuncio to the Philippines, Charles John Brown Also in the ceremonies were the two surviving bishops of Malolos, Dennis Villarojo, and Caceres Archbishop Rolando Tria Tirona, and bishops who served or came from the diocese.

On February 27 up to March 2, 2023, the diocese hosted the 29th Canon Law Society of the Philippines [CLSP] National Convention.

On February 14, 2024, Luneta Morales, a choir member, 83 years old was killed due to chest injuries while 63 attendees suffered multiple injuries when the "Vicariate of Saint Joseph" Saint Peter the Apostle Church (San Jose del Monte, Bulacan) 30-year old balcony-gallery, weakened by infesting termites collapsed during an Ash Wednesday service past 7 a.m. Dennis Villarojo said "those affected and their families are being assisted by the Diocese of Malolos with parish priest Fr.

He was installed as the fifth Bishop of Malolos on August 21, 2019, by Luis Antonio G. Tagle, then Archbishop of Manila as the metropolitan of the diocese, and Gabriele G. Caccia, then Apostolic Nuncio to the Philippines.