Based on what we've known so farEdit
- According to the Penguins of Madagascar series, the Penguins, Lemurs, and Chimps are still in their habitats in the Zoo, which is still open, but possibly, the absences of Alex, Gloria, Melman & Marty are caused by the circus & the Penguins were probably involved in something that reopened the Zoo
- In the film, the filmmakers purposely made it the same time of year it was at the beginning of the first film, at the end of this film... that way the city was JUST like it was before they left.
- The official junior novelization of the movie mentions the Penguins using a giant mechanical penguin-bot to fight Dubois in the climactic final scene, which Skipper refers to as having been built in anticipation of Y2K but was never used in the end. This never actually takes place in the movie, presumably to Kowalski's chagrin.
- Kowalski's iconic abacus makes its second appearance in the films.
- During the movie, you could see animals from the previous movies and series.
- The way the plane crash lands is the same way it did in the second movie.
- A reference to the first movie is made in the way DuBois and her men are stacked up in crates in the same way Alex, Marty, Melman and Gloria are stacked up in the first movie.
- Alex's birthday at the beginning of the movie is the same as Marty's in the first one. But, the wishes are different. In the first movie, Marty wishes he could go to the wild. But, in the third movie, Alex wishes he could go back to New York City's Central Park Zoo.
- This is the first time in the movies Julien saved the day.
- The ship from the first film reappears although it should still be on Madagascar. Then again, a possible reason for this is that it was found by a visitor to Madagascar, although this still does not entirely explain the reason.
- Marty's "Afro Circus" song has become a popular fad on YouTube, being used in remixes and edited videos.
- Zuba and Florrie were originally supposed to appear but they were cut. If they did appear Sherri Sheperd would reprise her role as Florrie and Samuel L. Jackson would've replaced Bernie Mac for Zuba.
- In the shot of New York's skyline shown in the scene the animals return to the zoo, the new World Trade Center towers are visible.
- In the international version, a Wilhelm Scream can be heard when a motorcycle rider crashes out of the freeway during the car chase scene.
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