IFCA International adheres to congregational polity in which each church is an independent, autonomous congregation governed by its own members. The denomination itself exercises no hierarchical control over member churches; rather, it serves as a fellowship and association of like-minded congregations. Each congregation is responsible for its own doctrinal purity, discipline, and practice, accountable to Scripture and the Lord rather than to a denominational headquarters.

The IFCA emphasizes sola scriptura — Scripture alone is the ultimate standard of faith and practice. No church tradition, denominational pronouncement, or human wisdom may supersede the authority of the written Word of God. The denomination has issued position statements and historical documents to guide member churches, but these are subordinate to Scripture and subject to revision if shown to be inconsistent with God's Word.

Ecclesiastical separation — the refusal of fellowship with churches deemed theologically compromised — is a distinctive IFCA principle rooted in fundamentalist theology. The IFCA practices secondary separation, declining fellowship not only with churches teaching false doctrine but also with churches that maintain fellowship with the theologically unfaithful. This reflects the conviction that doctrinal purity and biblical faithfulness are nonnegotiable.