Cornerstone Baptist Church was founded by Dr. Roberto-Jose M. Livioco on April 21, 1983. The first service was held in a small apartment in Project 8, Quezon City with only Pastor Livioco's wife, Imee in attendance. The following week's attendance increased by a hundred percent because of the visit of one of his converts. Soon, more were added to the flock. Because the growing number of people could no longer be accommodated in the apartment, Pastor Livioco led the church to its new meeting place at the PhilAm Homes clubhouse in West Avenue, Quezon City.

In 1985, rising rental costs forced the church to transfer to the Quezon Memorial College (QMC) along Tomas Morato Avenue, where they would spend the next ten years. While at QMC extensive soul winning efforts were done. The church prayed and labored hard to win souls to Jesus Christ. Among those who were won to the Lord and added to the church were relatives, friends, and classmates, while others were cold contacts. In 1993, Pastor Livioco received a call to pastor Grace Bible Church, Manila. After much prayer he decided to accept the call. On June 6, 1993, the pastorate was handed over to Jed B. Raquintan, a pastoral staff since 1989.

It was during the first three months of Pastor Raquintan's pastorate that the church was beset with the problem of rebellion instigated by the new pastor's colleagues. This led to the disciplinary action against and eventually to the excommunication of about a dozen members. But considering that the church then had only 35-40 active members, those who were disciplined were already a big part of the entire body. But it was, indeed, purging time, as those who remained saw it. Such situation did not dampen the spirit of those who stood by the pastor. Instead, it stirred them to intensify their soul winning efforts while at the same time protecting the weak brethren who were being led astray by the erring brethren. The pulpit was extensively used to set on fire the souls of the brethren to keep on doing the work of the Lord despite the opposition. By the Lord’s grace, the church survived the crisis.

In 1994, a charismatic group moved into the QMC compound, just a few meters away from the library where CBC was staying. The noise being created by the group during their services, which coincided with CBC's morning services, prodded Pastor Raquintan to look for another place to rent. While scouting for a place to lease, he began praying for funds to buy a lot and building that would permanently house the church. It was at this point that he also saw the need to register the church with the Securities and Exchange Commission (SEC). Thus, in December, 1994, Cornerstone was officially registered with the SEC as a religious corporation sole under the name Senior Pastor of Chief Cornerstone Fundamental Baptist Church, Inc.

On the first Sunday of December, 1995, CBC transferred to the Puzon Building right in front of a big Catholic church in New Manila, Quezon City. As soon as the church moved in, Pastor Raquintan initiated the lot and building project. It was decided that the funds would be raised indigenously, that is, no support-raising would be done through other churches and para-church organizations, either locally or abroad. Money must be raised within the congregation. The lot located in a subdivision in Tandang Sora, Quezon City, which was fully paid in 1997, is a testimony to the faithful giving of Cornerstone members which had grown to around 70.

The years 1997-2000 were sowing time for Cornerstone. Many Bible studies were opened in different areas in Metro Manila. Missionary workers were fielded to Pangasinan and Cavite to steadily build the existing work there. Another mission work in Legazpi City was begun with Bro. Roy Raquintan at the helm. Reaping time came in 2001. The obedience of Bro. Roland Niar to serve the Lord full-time as a member of the pastoral staff was a big boost to the church’s efforts to bring more people to the saving knowledge of Jesus Christ. The church had a steady growth from this time on.