The Brethren in Christ affirm the Holy Spirit as the third person of the Trinity, personal and divine. The Spirit's primary work is to apply redemption to believers, enabling their conversion, justification, sanctification, and perseverance in faith.

The Spirit empowers believers for Christian service and provides gifts for the edification of the church. However, the Brethren in Christ are cautious about certain charismatic practices, particularly glossolalia (speaking in tongues). While not denying that the Spirit may give any gift, they do not affirm tongues as a sign of Spirit-filling or as a normative expectation.

The denomination teaches that the Spirit indwells believers, provides conviction of sin, bears witness to the believer's adoption as a child of God, produces the fruits of holiness, and guides the community of faith in discernment. The Spirit's work is inseparable from Scripture and the church community; private spiritual experience is tested against biblical revelation and corporate wisdom.