- The film take place right after the events of Madagascar 3: Europe's Most Wanted.
- The TV Series with the same name takes place in a seperate continuity, better yet a parallel universe. Therefore, the TV series is non-canon.
- This is also technically the fourth Madagascar film, since it takes place after the third film.
- This is the only Madagascar installment where John DiMaggio doesn't voice Rico.
- This is the second film to begin the movie with a prequel. The first being Madagascar: Escape 2 Africa.
- In this film, Private is 10 years old, like Marty in the first film.
- This is the last film made by PDI before it got shut down in 2015.
- Dave has a purple Boeing CH-47 Chinook helicopter
- Dave's submarine resembles an octopus as it moves thru the water.
- running gag: Skipper keeps forgetting Dave's name.
- Apparently, The North Wind has had it's computer system hacked into before. The villains that hacked into their system before also had trouble with the microphone and video-feed as short fuse comments that, "every-time a villain calls in this happens."
- After Rico is swallowed the egg form of Private, Rico and the rest of the penguins fell to the iceberg then the egg form of Private is outside.