The ECC practices congregational polity with denominational oversight. Local churches are understood as autonomous communities of believers gathered in a covenant relationship. Each congregation exercises significant authority in its own governance, including the selection of pastors, the setting of local budgets, and the determination of worship and practice. However, congregations exist in covenant relationship with the ECC and recognize the authority of the denomination in doctrinal matters, ordination standards, and denominational discipline.

The ECC Covenant (the denominational document) and the affirmations of faith provide doctrinal boundaries within which congregational autonomy operates. The denomination does not control doctrine in an authoritarian way, but it does maintain standards and hold congregations accountable to core evangelical convictions. Regional conferences and the general assembly provide denominational governance and enable mutual accountability.

The authority of Scripture is supreme, but the ECC emphasizes that Scripture is interpreted within the community of faith. Believers are encouraged to read and study Scripture individually, but interpretation occurs in dialogue with the church's tradition, contemporary scholars, and the collective discernment of believers. This communal approach to biblical authority reflects the ECC's Pietist heritage, which values both personal faith and community wisdom. Women's ordination, affirmed since 1976, reflects the ECC's commitment to hearing the voice of the Spirit in the church regardless of gender.