The following are noted differences between the City of Bones novel and the movie adaptation.
| Book | Movie |
|---|---|
| Clary Fray was 15 years old and just turned 16 after Jocelyn went missing. | Clary Fray was instead 17, turning 18.[1] |
| Simon Lewis's eyes are brown. | Simon Lewis's eyes are green. |
| Isabelle led the Eidolon demon into a storage room at the Pandemonium Club. | Jace, Alec, and Isabelle kill it in the middle of the nightclub. |
| The Frays' apartment was indeed trashed in search of the Cup. | The apartment was in a seemingly worse condition because of the confrontation between Jocelyn, Samuel Blackwell and Emil Pangborn. Clary later went back to fix the damage with a rune. |
| Clary killed the demon in her apartment by shoving a Sensor down it's throat. | Jace killed the demon, though Clary Fray does make it weak by causing it to disintegrate in a kitchen explosion. |
| The Ravener Demon resemble "a cross between an alligator and centipede". | The Ravener Demon is in the form of a dog and becomes a sort of mutant octopus dog cross, yet its tendril's somewhat resemble the long body described in the book. |
| Jace, Clary and Simon searched Luke's bookstore and hid when Luke arrived, casually talking to Pangborn and Blackwell. | When Clary and Jace entered Luke's, leaving Simon outside, Luke is already inside and is being tortured by Pangborn and Blackwell. Clary asks Jace to save him. A fight breaks out. |
| Vampires are beautiful, white-skinned, and passable as mundanes. | Vampires resemble rotting zombies, albeit a bit more alive. |
| Simon Lewis is turned into a rat by a potion. | Simon does not get turned into a rat, but is drugged and used as bait to lure Clary and the other Shadowhunters into Hotel Dumort. |
| Only Clary and Jace rescue Simon from Hotel Dumort. | Alec and Isabelle join them to rescue Simon. |
| Raphael Santiago led Jace and Clary into the Hotel Dumort to rescue Simon. | Jace, Clary, Isabelle and Alec enter the Hotel Dumort through the front door. |
| Luke sends members of his pack to follow Clary and is not in the hotel fight. | Luke is part of the raiding group and the hotel fight. |
| Simon did not become a vampire until City of Ashes. | Simon has already showed signs of becoming a vampire in the film: his eyesight has gotten better and he has two bite marks on his neck. |
| There is no mention of famous figures being Shadowhunters. | Johann Sebastian Bach is a Shadowhunter, whose music can expose demons. |
| There is a portal in Madame Dorothea's flat. | There is a portal in the New York Institute. |
| Clary asked Simon to borrow Eric's van and to drive them to Madame Dorothea's. | Clary, Jace, Isabelle and Alec traveled to Madame Dorothea's on their own without Simon, though they run into Eric on their way. |
| Jace, Isabelle and Alec find out that Madame Dorothea is a demon when she opens the Portal in her room. | Suspicious, Jace plays a tune on Madame Dorothea's piano that distracts demons to find out if she was possessed by a one. |
| Simon helped kill the greater demon (Madame Dorothea) by using Alec's bow and arrow to destroy the skylight in the hallway. | Simon tackles Madame Dorothea through the front door of the apartment building after Clary told him she had the Cup. |
| Luke's pack resides in an abandoned police station. | They appear to be located in a car workshop called "Ed's Garage". |
| Clary Fray doesn't know she can make runes until City of Ashes. | Clary learns relatively soon that she can create runes. |
| Demons never entered the Institute. | Demons were brought into the Institute by Valentine. |
| Readers are led to believe that Jace and Clary are brother and sister. | Hodge gives Valentine the idea to lie to Jace and Clary about them being related. |
| Jace recognized Valentine as his father and did not fight him. | Jace's memories were apparently blocked, much like Clary's, and had to be "reminded" that Valentine raised him and is still doubtful afterwards. |
| Valentine Morgenstern's hair is white blond. | Valentine Morgenstern's hair is brown. |
| Clary followed Hodge Starkweather to confront him for giving Jace and the Mortal Cup to Valentine. He tried to kill Clary, but Luke saved her and Hodge disappears. | Hodge helps Valentine summon the demons but then helps Isabelle and Simon shut down the pentagram. |
| The fight at the end takes place at Valentine's lair. | The fight at the end takes place at the New York Institute. |
| The Mortal Cup is retrieved and hidden in Idris by Valentine. | Clary merely gave Valentine a replica of the Mortal Cup and was still in possession of the real one at the end of the film. |
| Valentine willingly entered the portal to Idris. | Clary Fray had to push Valentine into the portal. |
| Alec recovered and forgave Clary for their previous argument. | Alec is last seen still being treated by Magnus Bane. |
| Clary Fray had no luck getting a sign that her mother would wake up. | Clary found her mother at the Institute and her mother's finger quivered under upon Clary's touch. |
| When escaping Hotel Dumort, Jace takes Clary for a ride with a vampire's bike before sunrise above the river of New York. | Jace comes by Clary's house with a normal bike and takes her back to the Institute. |
| Valentine did not know that Jocelyn was pregnant with their second child until years after. | In a deleted flashback scene, Jocelyn's belly had already grown quite big while she was still with Valentine. |