Report of Proceedings: Secret Doctrine Centenary (Theosophical University Press, 1989) includes a presentation by Johnson, "The Chaldean Book of Numbers".
In Search of the Masters (self-published, 1990) contains material that was later reworked into the following:
The Masters Revealed (SUNY Press, 1994) attempts to recover the identities of the Theosophical Mahatmas. Where most non-Theosophical commentators assume them to have been invented by Mme. Blavatsky, and Theosophical ones believe them to have actually existed as described, Johnson proposes a third way of understanding the Mahatmas—as disguised versions of real, historical figures whom Blavatsky met during her travels.
Initiates of Theosophical Masters (SUNY Press, 1995), a sequel to the above (though less focused on Theosophy). Includes material on Radhasoami, the Baha'i religion, and the Fourth Way, all of which share Theosophy's interest in Oriental spiritual masters. Johnson approaches all of these spiritual movements from a skeptical point of view, though not in an attempt to debunk them.
Edgar Cayce in Context (SUNY Press, 1998). Examines various aspects of a well-known Kentucky clairvoyant. Johnson admires some aspects of Cayce (such as astrology, ESP, and his interpretation of Jesus), more than others (such as his "pseudo-history" or his prophecies).
The Inner West (Tarcher/Penguin, 2004) is a collection edited and introduced by Jay Kinney, including a chapter by Johnson, "Blavatsky and Her Masters."
Dictionary of Modern American Philosophers (Thoemmes, 2005) includes an entry on Helena Petrovna Blavatsky authored by Johnson.
Dictionary of Virginia Biography, Vol. 3 (Library of Virginia, 2006) includes an entry on Edgar Cayce written by Johnson.
Pell Mellers: Race and Memory in a Carolina Pocosin (Backintyme, 2008, 2013) combines family history and memoir in an investigation of mulatto ancestors and Union sympathizers in eastern North Carolina. The 2013 second edition includes an addendum describing Melungeon Unions of the previous five years.
Carolina Genesis: Beyond the Color Line (Backintyme, 2010) is a collection edited and introduced by Scott Withrow. The final chapter "Dismal Swamp Quakers on the Color Line" continues Johnson's investigations of North Carolina family and political history.
In 2012 the Typhon Press announced a forthcoming definitive edition of Ghost Land by Emma Hardinge Britten which Johnson co-edited with publisher Marc Demarest. In 2013 he announced plans to co-edit a collection entitled The Goinses with Stacy Webb for Backintyme Publications.