Iglesia ni Cristo reads Matthew 28:19 as authorizing baptism but emphasizes Acts' references to baptism 'in the name of Jesus.' Because the church is non-Trinitarian, the Trinitarian formula is understood differently: the 'Father, Son, and Holy Spirit' names refer not to three divine persons but to God's authority, the Son's role, and the Spirit's empowerment. The command to baptize is affirmed, but the ontological Trinity is rejected.

Baptism is practiced as immersion in water upon faith and is administered in the context of Iglesia ni Cristo's unitarian Christology. The baptismal formula emphasizes commitment to Christ and entry into the true church.