Jones, along with inker John Beatty, first collaborated with writer Moench on a series of Batman tales including Batman: Dark Joker the Wild and the vampire Batman trilogy beginning with Batman & Dracula: Red Rain. Both of these comics were very dark and moody, even for a Batman comic, crossing into horror. Batman fans were mixed as to Jones' run on the regular Batman book (1995–1998), some praising his dark and Gothic portrayal of Batman, and others thinking that his style was too radical. Going for style and mood over realism, Jones is known for drawing the ears on Batman's cowl and Batman's cape incredibly long, giving him a demonic look. Jones remained on the title until issue 552.
In addition to his run on Batman, Jones also illustrated the "Dream Country" and "Season of Mists" story arcs for Sandman, his style lending itself well to a story in which the main character must travel to Hell to free a former lover. Jones is also well known for revamping the character Deadman in the late 80s, redesigning him to look thin and skeletal. His face, formerly drawn to resemble a normal human's head with pale white skin, now looked like a skull. More recently, Jones has drawn the series The Crusades for Vertigo Comics (2000–2001), and the four-issue mini-series Conan: The Book of Thoth for Dark Horse Comics with writers Kurt Busiek and Len Wein in 2006.
Since 1997, Jones has also produced a number of works as a writer-artist for Dark Horse, including several miniseries and one-shots starring his creation The Hammer (1997–1999): the one-shot ZombieWorld: "Eat Your Heart Out" (1998; later included in the 2005 trade paperbackZombieWorld: Winter's Dregs), and the four-issue miniseries The 13th Son (2005–2006). He is currently working on illustrating the graphic novel adaptation of The Messengers for Dark Horse.
In 2008. Jones returned to illustrate the character Batman, this time in a twelve-issue series entitled Batman: Gotham After Midnight, written by Steve Niles. In 2009, he again illustrated Batman in a five-issue series entitled Batman: The Unseen, re-teaming with writer Doug Moench.
^Manning, Matthew K.; Dolan, Hannah, ed. (2010). "1990s". DC Comics Year By Year A Visual Chronicle. Dorling Kindersley. p. 251. ISBN978-0-7566-6742-9. "Written by Batman alumnus Doug Moench, and illustrated with the shadowy pencils of Kelley Jones, Red Rain chronicled the clash between Batman and the legendary Dracula."