Starting in this film, All Effects Company took over and worked on the animatronic effects for the turtles and Splinter costumes. Jim Henson's Creature Shop was the company who worked on the mutant creatures in the previous two movies.
Mark Caso (The performer inside the Leonardo costume), is the only cast to return from Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991). Brian Tochi (The voice of Leonardo) and Robbie Rist (The voice of Michaelangelo) are the only actors who appeared in all three movies in the trilogy. Corey Feldman who appeared in Teenage Mutant Ninja Turtles (1990) makes his return as the voice of Donatello.
Producers invited Corey Feldman to reprise his role from the first film as Donatello. The filmmakers told Corey they felt bad about not casting him for Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991). However, when Corey asked for more money than the $1500 he was paid on Teenage Mutant Ninja Turtles (1990), Corey was told, "yeah, but you were in rehab." Corey was denied the raise, and was again paid only $1500.
This film was originally going to be followed by a fourth installment in the franchise, "TMNT: The Next Mutation." In this concept, the Ooze that transformed the Turtles and Splinter was still in their bodies, causing a much more drastic second mutation. Another plan that was discussed was to add a fifth turtle named Kirby (named after comic artist Jack Kirby). However, the project got stuck in development and plans for a fourth theatrical live action movie fell apart. The concept of having the Turtles mutate into creatures did see the light of day in the 'New Mutation' saga of the Teenage Mutant Ninja Turtles (1987) cartoon. Later, the live action "Next Mutation" installment moved to television in a live-action series produced by Saban, titled Ninja Turtles: The Next Mutation (1997). This series delivered on the promise of a fifth turtle, but changed it to a female turtle named Venus De Milo.
In the original comics, the Time Scepter is normally associated with Renet, the time apprentice of Lord Simultaneous. She often encounters Savanti Romero. None of these characters appear in this film.