On September 20, 1954, His Eminence Rufino Cardinal Santos, the Archbishop of Manila, officially divided Manila into four Chinese parishes.  These were San Lorenzo (Binondo), Mary the Queen (Greenhills), St. Jude (San Miguel) and St. Peter the Apostle (Paco).  Fr. Jacques (James) Mussen, CICM became the St. Peter the Apostle Parish priest that year.  With the help of the parishioners, a permanent church was built to replace the small chapel. He was assisted by Fr. Dominic Kuo, a young Chinese priest.  Later, Fr. Kuo was appointed as the National Director for the Chinese Catholic Youth from 1963-1966.

Fr. James Mussen served as parish priest for 13 years.  He was succeeded by two more priests, namely Fr. James Libeer, CICM (1971-1972) and Fr. Joseph Liu, CICM (1972 to 1974). 

On December 22, 1974, Fr. Vincent Liu, a diocesan priest from New York became the parish priest.  Fr. Liu took it upon himself to establish a school that would provide a Catholic education with Chinese instruction for the Filipino-Chinese community in the parish.   He met with a small group of active and loyal parishioners for the purpose of raising funds for the construction of a school building.  The group included Mrs. Conchita Gan, Mr. and Mrs. Enrique, Ms. Eva and Elena Cuatico, Mr. and Mrs. Domingo, Mr. and Mrs. Maximo Tan, Mr. and Mrs. Jose Bautista, Mr. and Mrs. Gabriel Yuching, Mr. Martin Lee Sunga, Mr. and Mrs. Faustino (Alo) Dee, Ms. Flora Go, Miss Rosario (Ching) Sevilla, Mr. and Mrs. Patrick Ng, Mr. Mariano Dee and Mrs. Mary Kun. Of the many benefactors, the top four were the late Jaime Cardinal Sin (Archbishop of Manila), Mr. Ralph Nubla (Philippine Bank of Communications), Mr. Lucio Tan (Allied Banking Corporation) and Mr. Emilio Yap, Sr. (Philtrust Bank and Manila Bulletin). 

On June 14, 1976, St. Peter the Apostle School (SPAS) opened its doors to the youth of the parish with Fr. Vincent Liu as its first Director.  With the support of the Archbishop of Manila and the members of the Parish Council, Fr. Liu started to raise funds for the construction of a four-story school building to house the growing school, which was offering grade two by then.  On November 6, 1977, the groundbreaking ceremony of laying down the cornerstone of the new school building was held.  Both His Eminence Cardinal Sin and Bishop Velasco were present at the ceremony. On February 4, 1979, the new SPAS school building was inaugurated by His Eminence Jaime Cardinal Sin and Bishop Juan Velasco. 

 By the beginning of the 1980’s, Fr. Vincent Liu had to fly to the United States for health reasons.  Thus, on August 1, 1981, Fr. Francis Chin took over as new parish priest and director of the school.  

 Metro Manila was rudely shocked with a strong earthquake in July 1990.  The calamity caused damaged to the church.  Reconstruction was carried out to repair the damage and make the place safe for its growing population. 

On August 23, 2003, His Eminence Jaime Cardinal Sin blessed the majestic new St. Peter the Apostle Church.  The space once occupied by the old church is now the school playground. 

In July 2012, Rt. Rev. Msgr. Noly A. Que, LRMS, MBA, PhD became the Director of the school and the Parish Priest of St. Peter the Apostle Parish.  The Msgr. Francis Chin Mini Park was built near the playground. A new parish office was constructed at Gate B (near the Church).

This school year 2014-2015, Msgr. Noly Que was appointed by the Archdiocese of Manila as the Father Moderator.  Fr. Emilio A. Ascaño, LRMS became the new Director of St. Peter the Apostle School and Fr. Emmanuel S. Regalado, LRMS took over the duties of Financial Officer from Fr. Zhu.  Fr. Junerl A. Salugusugan, LRMS continues as CCF Head and Campus Minister.