Four years after the creation of the Diocese of Lipa in June 1914, Bishop Giuseppe Petrelli, Lipa’s first bishop, founded St. Francis de Sales Seminary as a College-Seminary, with the help of the Spanish Vincentian Fathers (Padres Paules), at San Pablo, Laguna, transferred four months later to Bauan, Batangas.

In June 1917, Bishop Alfredo Verzosa, Lipa’sm second bishop, brought back the College-Seminary to San Pablo, considering that the said town was more to the center of the five-province diocese – Tayabas, Marinduque, Batangas and the two Mindoros. On March 20, 1918 it was recorded that the Congregation of the Missions (CM), the Vincentian Fathers in the Philippines, loaned the amount of 30,000 for the construction of the College-Seminary in the Diocese of Lipa.

Following the example of the Archdiocese of Manila, Lipa’s mother diocese, Bishop Verzosa decided in March 1923 that St. Francis de Sales Seminary should exist only as a residential seminary exclusively for those training towards the holy priesthood. In May 1931, Bishop Verzosa transferred the Major Seminary (College and Theology Departments) to Lipa, resigning his palatial residence to the seminarians and the Spanish Vincentian Priests.

From 1931 on, the Major Seminary was called Seminario de San Alfonso de Ligorio whose first rector was the Rev. Fr. Alfonso Saldaña, CM.

The climax of the most destructive war in the country in February 1945 changed the history of Lipa. The Cathedral of St. Sebastian and the Major Seminary, like the rest of the town, were completely destroyed. Nearly 19,000 civilians were massacred in Lipa alone, while the Padres Paules of Manila also lost the lives of many of their confreres, disabling them to continue the administration of Lipa’s Seminario de San Alfonso de Ligorio.

True to its ministry of priestly formation, the Diocesan Seminario Mayor de San Alfonso reopened in Batangas, Batangas in July 1945 where both seminarians and the all-Filipino diocesan priests faculty members, with Rev. Fr. Angel Glinoga as rector, lived and studied in the army barracks abandoned by the U.S. military liberation forces. In 1949 after a fire and explosion near the Batangas Seminary, Seminario de San Alfonso de Ligorio returned to Sabang, Lipa.

In 1950, at the resignation of Bishop Verzosa, Bishop Rufino Santos was appointed Administrator of the Diocese of Lipa. He invited the priests from the Congregation of the Immaculate Heart of Mary (CICM), better known locally as the Belgian Padres, to take over the administration of Lipa’s Major Seminary. It was renamed St.Francis de Sales Major Seminary and located at the newly constructed building in Sabang before it transferred to a more permanent building in Marauoy, Lipa City, Batangas. Rev. Msgr. Jose Billiet, the former Apostolic Vicar of Mountain Province (Baguio) was appointed Rector of St. Francis de Sales Major Seminary; and the rest of the Faculty were CICM priests. When in 1953 Bishop Santos was recalled from Lipa to become the Archbishop of Manila, he took with him the Belgian Fathers and assigned them as the administrators of the newly built San Carlos Seminary in Highway 54, now called EDSA. The then recently designated Archbishop of Manila also
took with him the entire seminarian-student body from the Philosophy and Theology Departments, leaving St. Francis de Sales Seminary orphaned of the higher studies for priestly training. Only the Minor Seminary in Bauan, that later transferred to Marauoy, survived the harsh changes in the post war decade in the Diocese of Lipa.

In his desire to recover the old tradition of priestly formation for the clergy of Lipa, Bishop Alejandro Olalia decided in 1965 to reopen the Philosophy Department at the northern wing of the seminary building in Marauoy. In 1999, the Archdiocese of Lipa, under the guidance of Archbishop Gaudencio Rosales, began sending priests to Rome to do post-graduate studies in Theology as preparatory for the refounding of the St. Francis de Sales Theological Seminary (SFSTS). In June 2003, the Theology Department finally reopened and in 2008 the first ordinations to the sacred priesthood from SFSTS were administered by Lipa’s eighth local ordinary, Archbishop Ramón Argüelles. On September 8, 2014, Archbishop Luis Antonio Cardinal Tagle of the Archdiocese of Manila, together with other bishops, blessed the SFSTS chapel and the building’s right wing which houses the faculty and the seminarians’ residences.