The index has three parts: subjects, persons, and Scripture. Each locator points to the section in which a topic, person, or passage is discussed. In the printed and PDF book it gives the page on which that section begins, and the discussion lies on that page or within the next few pages. In the electronic edition each locator is a chapter number linked to the section itself.

In the subject index, bold numbers mark a section in which the topic is a principal subject. An asterisk after a heading (*) means that the term is defined in the Working Lexicon, Appendix E, where entries run alphabetically. "Claim" followed by an identifier points to the Claim Index and Argument Map in Appendix B, where each claim's grounds, limits, and dependencies are stated. Biblical figures appear among the subjects; ancient and modern authors and other historical persons appear among the persons.

The Scripture index lists every passage cited by chapter or verse in the text and its notes, in canonical order, with the deuterocanonical books between the testaments. Passages named only as whole books, such as Job, the Psalms, or Revelation, are indexed among the subjects where the book itself is discussed.