Although known mostly for his work under prosthetic makeup, such as the zombie William "Billy" Butcherson in the Walt Disney Pictures Halloween film Hocus Pocus, or the lead spy Morlock in the 2002 remake of the 1960 film The Time Machine, he has also performed without prosthetics in such films as Adaptation, Mystery Men, and Batman Returns, and indie projects such as Stefan Haves' Stalled, AntiKaiser Productions' Three Lives, Phil Donlon's A Series of Small Things, and as Cesare in David Fisher's 2005 remake of the 1920 silent classic The Cabinet of Dr.

Working once more under heavy prosthetics in both roles, he was also required to learn large amounts of dialogue in Spanish,[9] although ultimately his voice was redubbed by Pablo Adan.

He reprised his role as Abe Sapien in Hellboy II: The Golden Army, once more under the direction of del Toro, for which he provided both the voice and body performance.

As Jones gained greater clout in the industry, he eventually was able to add a clause to his contracts ensuring that no English dialogue of his characters would be dubbed.

[13] Jones appeared in the French-language film Gainsbourg (Vie héroïque), written and directed by French comic book author Joann Sfar and produced by Universal Europe.

Jones played La Gueule ("The Mug"), the grotesque fantasy muse and malicious doppelganger who teases, guides, and accompanies Serge Gainsbourg throughout his life.

[14] He was fitted with prosthetics designed and created by the Academy Award-winning Spanish FX shop DDT Efectos Especiales, with whom he had already worked on Pan's Labyrinth; the FX technicians requested specifically that Jones be given the role of the Mug creature, due to his ability to perform (without complaining)[12] with heavy prosthetics and elaborate special effects.

As in Pan's Labyrinth, Jones performed his lines phonetically, this time speaking in French; his voice was redubbed by Éric Elmosnino, who also played Gainsbourg.

Director Joann Sfar liked Jones's speech patterns so much that he asked Elmosnino to mimic them when he performed the creature's lines.

That same year, Jones reunited with Guillermo del Toro, this time in a romantic lead role, the Amphibian Man (the "asset") in the Academy Award-winning The Shape of Water.

[25][26] Jones describes himself as a "dyed-in-the-wool Christian from the Midwest", to the point that he was initially apprehensive about his role in Hellboy due to the titular character's demonic nature.