A car bears the license plate "Mirage84". The Teenage Mutant Ninja Turtles first appeared in Mirage Comics in 1984.
Brad Garrett, who voices Krang in this film, is best friends with Pat Fraley, who voiced Krang in Teenage Mutant Ninja Turtles (1987). Fraley personally endorsed Garrett as Krang when he was announced.
When Casey Jones is smashing up the bar, "Ice Ice Baby" by Vanilla Ice is heard on the jukebox. Vanilla Ice appeared and performed "Ninja Rap" in Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991).
The mutagen in this film is purple instead of the common green-colored mutagen. This came from Teenage Mutant Ninja Turtles (1987), which featured different varieties of mutagen that formed different mutants.
Splinter is designed to have grayer fur and a brown robe in this film, in homage to his appearance in Teenage Mutant Ninja Turtles (1990) and Teenage Mutant Ninja Turtles (2003).