In the next phase of his career, he departed from martial arts writing and wrote several books on the folklore and beliefs of the occult and paranormal, including The Vampire Slayers Field Guide to the Undead (Strider Nolan, 2000), written under the pen name of Shane MacDougall; Vampire Universe: The Dark World of Supernatural Beings That Haunt Us, Hunt Us and Hunger for Us (Citadel Press, 2006); The Cryptopedia, co-authored by David F. Kramer (2007); Zombie CSU: The Forensics of the Living Dead (2008); They Bite (also with David F. Kramer, 2009); and Wanted Undead or Alive (with Janice Gable Bashman, 2010).

He moved to Dark Horse Comics and produced a single miniseries, Bad Blood, with artist Tyler Crook, which went on to win the Bram Stoker Award for Best Graphic Novel.

His bestselling work was the novelization of the 2010 film The Wolfman which starred Benicio del Toro, Anthony Hopkins, Emily Blunt, and Hugo Weaving.

In the second book, The Dragon Factory, the villains are geneticists using cutting-edge science to restart the Nazi master race eugenics program.

The series' main publisher, Griffin, released Joe Ledger: Unstoppable, an anthology of Ledger stories written by a variety of top suspense and mystery writers including Tim Lebbon, Scott Sigler, Steve Alten, Weston Ochse, Dana Fredsti, Christopher Golden, Joe McKinney, Jeremy Robinson, Javier Grillo-Marxuach, Sherrilyn Kenyon, Bryan Thomas-Schmidt, and others.

In 2015 Maberry released a rare standalone novel, Ghostwalkers, based on the Deadlands table top role playing game.

Although a standalone, Ink has elements of other books, including characters and locations from the Pine Deep Trilogy, and the appearance of Monk Addison and Patty Cakes from Glimpse.

Also in 2017, Maberry published Indigo, a collaborative work of fiction written with nine other authors including Charlaine Harris and Christopher Golden.

[21] Maberry is also a contributing editor for The Big Thrill,[22] the monthly newsletter of the International Thriller Writers, and a founding partner of The Liars Club, a networking group of professionals in publishing and other aspects of entertainment.

[23] Date Zero Tolerance Deep, Dark Material Witness Dog Days Doctor Nine Property Condemned Adventure of the Greenbrier Ghost Cooked Penguin Group Jo Fletcher Books Wheeler Publishing Brilliance Audio A Zombie Anthology Chokepoint Pegleg and Paddy Save the World The Wind through the Fence Zero Tolerance Deep, Dark Material Witness Changeling Mad Science Artifact The Handyman Gets Out Borrowed Power Inside the DMS Interview with Ray Porter Mister Pockets Property Condemned Whistlin' Past the Graveyard The Trouble The Death Song of Dwar Guntha Plan 7 From Sin City Clean Sweeps The Vanishing Assassin The Adventure of the Greenbrier Ghost Calling Death Flint and Steel The Death Song of Dwar Guntha Chokepoint Clean Sweeps Long Way Home Mister Pockets Property Condemned Whistlin' Past the Graveyard Cooked The Death Poem of Sensei Ōtoro Ink Atoll Blackstone audio collection Plan 7 from Sin City.

Red Dreams Saint John Spellcaster 2.0 She's Got a Ticket to Ride The Cobbler of Oz The Things That Live in Cages The Vanishing Assassin The Wind through the Fence Faces Fat Girl With a Knife Jingo and the Hammerman Son of the Devil