The book was written as an introductory textbook on the Protestant faith for those with some learning already and covered a broad range of theological topics from the doctrines of church and sacraments to justification by faith alone and Christian liberty, and it vigorously attacked the teachings of those Calvin considered unorthodox, particularly Roman Catholicism to which Calvin says he had been "strongly devoted" before his conversion to Protestantism. The over-arching theme of the book – and Calvin's greatest theological legacy – is the idea of God's total sovereignty, particularly in salvation and election.

The Institutes are a primary reference for the system of doctrine adopted by the Reformed churches, usually called Calvinism.