By the late 1990s, FBC had grown to the extent that restructuring was a real issue to be faced. Desiring to maintain the congregational type of government, while decreasing the number of meetings and day-to-day decisions by the whole body, a plan was presented to the church in 1998, and adopted in 1999. It incorporated a Council, while still keeping the church business meeting over the entire structure. Though the church now meets less often, they must be consulted on major issues such as the direction and vision of the church, alterations of the church structure, calling of the Senior Pastor, and election of the Council, adoption of budget, and addition or secession of any congregation. In 1998, FBC became one large church with several centres, one comprising the original Pantai Centre and the other comprising the Subang Centre from mid-1991. Subang Centre became FBC when the original Subang Jaya Baptist Church was deregistered as a society in December 1990, almost losing the property that was in FBC’s name.
For the next two decades until June 2010, FBC grew strongly with increasing ministries in both centres. The Lord called faithful ministers to the FBC pastoral team – Pastor Tan Soo Inn, Pastor Isaac Yim, Pastor Mark Chen, Youth Pastor Chen Khin Wee, Pastor Joseph Seah, Pastor Tan Eng Lee, Pastor Phillips Koh, Pastor Ang Chooi Tuan, Pastor Thomas Ooi, Pastor Chua Soon Kent, Pastor Princeton Tay, Pastor Edward Ha, Pastor Ooi Aun Leong, Pastor Leong Swee Huat, and Youth Pastor Timothy Yap. Pastor James Indran and Pastor K Chandran served in the Ampang Tamil Baptist Church which was an outreach of FBC.
Pantai Baptist Church (PBC) shares a rich Baptist heritage with First Baptist Church (FBC) in Subang Jaya. PBC and FBC are two independent Baptist churches today that grew out of a common root, the seed of which was planted in the 1950s by missionaries from the Foreign Mission Board (now known as the International Mission Board) of the Southern Baptist Convention, USA (SBC). The missionaries, Jessie Green, Elizabeth Gray, Elizabeth Hale, Harold and Ann Clark set up a gospel centre and Baptist clinic in Jalan Dispensary, PJ Old Town. From this gospel outreach, FBC was established on 16 June 1957 as the first English speaking Baptist churches.