He was a member of both the Theosophical Society and the Association for Research and Enlightenment from the late 1970s intermittently through the early 2000s. In 2005 he joined the Church of Light (founded by C.C. Zain).
- 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 Blavatsky's 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. (The need for this dissimulation arose from the political situation of 19th-century British India, he says.) Johnson tentatively suggests a list of real-world spiritual figures (e.g., Thakar Singh Sandhanwalia, Ranbir Singh, Jamal al-Din al-Afghani, Swami Dayananda Saraswati, Sarat Chandra Das) who share various features in common with their putative counterparts. One casualty of Johnson's proposed revision is that unlike Theosophy's masters, these individuals had little in common with one another (or with Blavatsky), and seem to have lacked supernatural powers or authority.
- 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.
- K. Paul Johnson (2008), Pell Mellers: Race and Memory in a Carolina Pocosin, Backintyme, ISBN 9780939479283, http://books.google.co.uk/books?id=RMWqSRKSi70C ; Combines family history and memoir in an investigation of mulatto ancestors and Union sympathizers in eastern North Carolina.