The BFM2000 identifies the Holy Spirit as the third person of the Trinity, fully divine, coequal with the Father and Son. The Spirit was active in creation and in the inspiration of Scripture, and now convicts the world of sin, regenerates the sinner at conversion, indwells every believer, and sanctifies the redeemed throughout their lives. The Spirit is the divine presence who enables Christian living and empowers the church for witness.

The SBC does not officially require or endorse speaking in tongues as the normative evidence of Spirit baptism. In contrast to classical Pentecostalism, most SBC theologians hold a cessationist or cautiously open position regarding miraculous gifts — though individual churches vary in practice. The SBC's position is that the Spirit sovereignly distributes gifts according to His will for the building up of the church.

The BFM2000 also affirms that the Spirit illuminates Scripture and guides believers into truth. Southern Baptists maintain that the Spirit does not operate independently of Scripture, and any claimed Spirit-experience must be tested against biblical teaching.