The RCA organizes according to Reformed polity: the local church is governed by a consistory (council of elders); regional churches relate through a classis (regional assembly); and the general synod coordinates the whole denomination. Authority is distributed and representative, subject to Scripture.

The RCA affirms sola scriptura—Scripture is the ultimate authority in doctrine and practice—while recognizing the Three Forms of Unity as faithful summaries of biblical teaching. The RCA has experience significant internal debate regarding the authority of Scripture, particularly on questions of biblical inerrancy and the authority of biblical prohibitions.

A major point of tension in recent decades has been women's ordination. Permitted since 1979, women's ordination has divided the RCA internally and resulted in departures of conservative congregations. The denomination maintains that decision-making authority ultimately rests with local consistories, though the denomination officially permits and encourages women in leadership roles.