Eventually, Sto. Rosario was erected as a Parish with Msgr. Jose Ma. Cuenco as the first parish Priest in February 1933. The building was concrete and the main altar was made of exquisitely carved Philippine hard wood.

During the war years and Japanese occupation, the parish was run by Very Reverend Ernest Hoerdemann, SVD, a German national who was then attached with the Colegio da San Carlos. He was succeeded by Rev. Fr. Thomas Villamor, then by Rev. Fr. Cesar J. Alcoseba, followed by Msgr. Esteban Montecillo, who was appointed Vicar General to Archbishop Julio R. Rosales, who was installed as Archbishop of Cebu in 1949. At that time Sto. Rosario was made Pro-Cathedral up to July 1951 because the Cebu Metropolitan Cathedral was rebuilt after it was destroyed during the World War II.

In May 16, 1972. Msgr. Esteban Montecillo retired as Parish Priest after serving the Parish for 22 years. The new Auxiliary Bishop of Cebu, Most Re. Nicolas Mondejar, D.D. a native of Iloilo, took over as the Parish Priest. The latter was promoted as Bishop of Romblon and his assistant Rev. Fr. Esteban S. Binghay, J.C.D. took over in acting capacity. On February 10, 1976, a new Parish priest was appointed in the person of Right Reverend Frederick Kriekenbeek until June 1987.

In July 31, 1978, after much prayer and discernment from the holy spirit, the decision was made to demolish the old structure, and to lay the foundations of the new building. The whole parish was mobilized to raise funds for the new church. In  a period of ten months and as a testimony of the generosity of God's people, the new parish church was completed and the blessing undertaken by Cardinal Julio R. Rosales on June 2, 1979, on the occasion of his Silver Jubilee celebration. Msgr. Fred Kriekenbeek is much credited also for the formation and development of the Catholic Charismatic Renewal Movement.

In June of 1987 up to February 1998, Right Reverend Esteban S. Binghay assumed as Parish Priest after Msgr. Fred Kriekenbeek. For almost 11 years, changes and improvements have been done in the church for the comfort and efficient service to all parishioners and the people of God.

 Sto. Rosario was one of the city parishes on pilot study for the new parish management initiated by Cardinal Vidal, in the form of Parish Team Ministry. Thus, we have Bishop Jose S. Palma, Rev. Fr. Paquito F. Kintanar an Rev. Fr. Alex Lim as the first Team Ministry Ministry of the Parish, with Fr. Omen Mahusay, Parochial Vicar. For one year we had a smooth transition from the old system especially to cater to the spiritual needs of the parish at the grassroots level.

The sudden transfer of Bishop Jose S. Palma to Calbayog in March 1999 brought us Bishop John F. Du, senior moderator and Bishop Antonieto D. Cabajog, co-moderator was installed together with three parochial vicars: Rev. Fr. Felipe Diacosta, Rev. Fr. Glen Joseph De La Torre and Rev. Fr. Rizalino Michael Raypan. Under their administration, massive reconstruction of the sanctuary, rectory, 2nd & 3rd floors, Adoration chapel and Confessional rooms. The new Beato Pedro Calungsod Hall is used for conferences and other parish functions. All of these were due to the generous contributions of the parishioners, generous friends and donors. The blessings and dedication of the buildings was done on the Priest's sanctification day with a concelebrated mass attended by 240archdiocesan priests presided by His Eminence Ricardo J. Cardinal Vidal.