The ECC affirms the Holy Spirit as the third person of the Trinity — fully personal and fully divine, worthy of worship and trust. The Spirit's role in creation, redemption, and sanctification is affirmed. The Spirit works to convict sinners, call them to repentance, and transform them into the image of Christ. The ECC emphasizes the Spirit's ongoing role in the life of the church and of believers, guiding, comforting, empowering, and enabling growth in faith.

The ECC stands within a Pietist tradition that emphasizes the Holy Spirit's living presence and the believer's direct experience of God. This heritage makes the ECC open to charismatic renewal and the work of the Spirit in contemporary times. However, the ECC is balanced in this openness, maintaining that the Spirit's work must be consistent with Scripture and subjected to the church's discernment. The ECC does not mandate a specific view of spiritual gifts (tongues, prophecy, healing) but allows diversity of practice and conviction on these secondary matters.

The ECC teaches that the Holy Spirit indwells believers, produces spiritual fruit (love, joy, peace, etc.), and equips them for ministry and witness. The Spirit's presence is both personal experience and objective reality, both inward transformation and empowerment for service. Believers are called to be 'filled' with the Spirit, to grieve not the Spirit, and to cooperate with the Spirit's work through prayer, obedience, and submission.