In the 1970s as the parish population grew, there was a need to build a bigger church.
 The original stone church was expanded by removing the northeastern wall and the new nave was constructed northeastward  from the wall.
 With the renovation, the original church structure became the sanctuary space while the original facade and apse now appears like semitransepts of the present church.
They are separated from the present sanctuary by a reinforce concrete wall with a tall archway separated from the sanctuary by a wooden partitions.
 The former baroque altars became side altars and sacristy of the church.
 There was a huge crucifix at the center of the sanctuary and the floor was changed to marble.
 The church was built in accordance to the Second Vatican Council.

In 1989, the three-century old baroque altars were transferred to the main sanctuary in time for the celebration of the 400th anniversary of the founding of San Francisco del Monte on February 17, 1990.
 The dedication ceremony of the new sanctuary was headed by the Franciscan Superior of the order.
The 400th anniversary feast day celebration on February 17 was headed by Jaime Cardinal Sin, then the Archbishop of Manila.

On February 5, 1997, the parish marked the 400th Anniversary of the martyrdom of Saint Pedro Bautista.
Two murals were created to commemorate the life of the founder saint, on display on each side of the sanctuary.
The mural on the left side is that of the life of Pedro Bautista from Ávila, Spain to San Francisco del Monte, from teaching the natives the use of musical instruments to finding medicinal use for the natural springs of Los Baños, Laguna, from his arrival to the shores of Japan, to his death in Nagasaki.
The mural on the right is that of the martyrdom scene on the hill of Nagasaki.

On February 25, 2001, the parish church was declared an archdiocesan shrine and the name was changed to Sanctuario de San Pedro Bautista (Saint Peter Baptist Shrine) in view of its historical and religious significance to the Archdiocese of Manila.

In 2003, the Diocese of Cubao was created from the Archdiocese of Manila, and the church became part of the new diocese.
 The Diocesan Coat of Arms has a Tau cross on top of the hills as a reminder of the Franciscan missionary and martyr, Saint Pedro Bautista, who founded the mission and Church in San Francisco del Monte in the late 16th century before he was martyred in Japan.
In the 1970s as the parish population grew, there was a need to build a bigger church.  The original stone church was expanded by removing the northeastern wall and the new nave was constructed northeastward  from the wall.  With the renovation, the original church structure became the sanctuary space while the original facade and apse now appears like semitransepts of the present church. They are separated from the present sanctuary by a reinforce concrete wall with a tall archway separated from the sanctuary by a wooden partitions.  The former baroque altars became side altars and sacristy of the church.  There was a huge crucifix at the center of the sanctuary and the floor was changed to marble.  The church was built in accordance to the Second Vatican Council.
In 1989, the three-century old baroque altars were transferred to the main sanctuary in time for the celebration of the 400th anniversary of the founding of San Francisco del Monte on February 17, 1990.  The dedication ceremony of the new sanctuary was headed by the Franciscan Superior of the order. The 400th anniversary feast day celebration on February 17 was headed by Jaime Cardinal Sin, then the Archbishop of Manila.
On February 5, 1997, the parish marked the 400th Anniversary of the martyrdom of Saint Pedro Bautista. Two murals were created to commemorate the life of the founder saint, on display on each side of the sanctuary. The mural on the left side is that of the life of Pedro Bautista from Ávila, Spain to San Francisco del Monte, from teaching the natives the use of musical instruments to finding medicinal use for the natural springs of Los Baños, Laguna, from his arrival to the shores of Japan, to his death in Nagasaki. The mural on the right is that of the martyrdom scene on the hill of Nagasaki.
On February 25, 2001, the parish church was declared an archdiocesan shrine and the name was changed to Sanctuario de San Pedro Bautista (Saint Peter Baptist Shrine) in view of its historical and religious significance to the Archdiocese of Manila.
In 2003, the Diocese of Cubao was created from the Archdiocese of Manila, and the church became part of the new diocese.  The Diocesan Coat of Arms has a Tau cross on top of the hills as a reminder of the Franciscan missionary and martyr, Saint Pedro Bautista, who founded the mission and Church in San Francisco del Monte in the late 16th century before he was martyred in Japan.
Santuario de San Pedro Bautista