In the Miagani Island Botanical Gardens, there is a bench with a plaque saying "In Loving Memory... Dr. Alec Holland", referring DC Comics/Vertigo character, the Swamp Thing.

In Wayne Tower there is a dog bowl with the name "Ace" labelled on it. This is a reference to Bruce's dog in the comics, Ace the Bat-Hound.

A locker with a name "Ray Palmer" can be seen when visiting ACE Chemicals, with an atom symbol sketched on it. Ray Palmer is the real name of "The Atom", a hero from DC Comics.

During the story mission at Ace Chemicals after turning off the pipes to enter the lower level, just to the right of the obstacle is a clipboard with a vile labelled "Copperhead Poison." This is in reference to Copperhead from Batman: Arkham Origins.

If the player has already captured Spoiler:Man-Bat and the internal date of the system is set to October 31st, the player can trigger a jumpscare by him while trying to grapple atop a building. Going back to GCPD reveals that he has escaped.

There are two unused game over sequences for The Riddler that suggest that the player was originaly supposed to rescue hostages from him, similar to Batman: Arkham City.

In Wayne Tower, if Batman checks his answering machine long enough, a message from DC Comics character Lex Luthor will play, followed by a message from a lady named Kate Kane, aka Batwoman.

When reviewing the camera footage Spoiler:to find Barabara's kidnapper, Victor Zsasz, from the previous Arkham games, can be seen in footage among the other rioters.

One of the posters seen in Gotham throughout the game is for a film called "The Ghost in Gray" and features a man in a hat and goggles. An actor named "Simon Trent" is also listed on the poster. This is a reference to the Gray Ghost, a character from "Batman: The Animated Series" and the eponymous character of the episode "Beware the Gray Ghost." The Gray Ghost was an old TV superhero played in universe by Simon Trent, with his costume consisting of a fedora hat, goggles and trenchcoat. Bruce Wayne was a huge fan of the Gray Ghost series and character, with Ghost serving as inspiration for Bruce to become Batman. In said episode, Batman enlisted Trent's help (in costume as the Gray Ghost) to stop a criminal who was imitating a scheme used by one of the villains from an episode of the Gray Ghost series.

Additionally in the Batman Animated Series, Gray Ghost/Trent was voiced by Adam West, who played Batman in the 1960s TV series. Adam West's Batman costume is available in Arkham Knight as DLC.

Spoiler:During The Joker's nightmare sequence, the player can spot a painting of Batman carrying The Joker's body from the end of Batman: Arkham City. The painting itself is actually a piece of concept art from Arkham City.

The screens of the watchtower stations the player must destroy in the side mission: "Occupy Gotham", are actually recycled from the Cryptographic Sequencer's screen from Batman: Arkham Asylum.