There were outtakes of Jonah: A VeggieTales Movie that can be found on the VHS and DVD release.
- Dad, Bob and the kids are going down the hill avoiding the tree and cabin, then they hit LarryBoy, who says "Hi guys, what's up?"
- In the first shot, when Bob was saying his line, the porcupine shoots his hat off. In the next shot, the porcupine shot the cameraman. In the third shot, the porcupine hit the car which hit Bob.
- Junior and Laura burst out laughing during a scene where they're supposed to be arguing.
- In the first shot, the Pirates were saying their lines and Larry says "nothing," but Mr. Lunt corrects him. In the next shot, Larry says "Zilch." In the third shot, Larry says "Noodle," which results in Mr. Lunt hitting his head.
- In the first shot, the tape tells Jonah he's vain, and thinks the movie is all about him (a reference to the Carly Simon song "You're So Vain"), and laughs. In the next shot, the tape tells a joke, and cracks up.
- After Jonah says his line, Khalil tries to get out, but the bag fails to break, and he instead falls over and screams for help.
- In the first shot, Bob announces a rest-stop while Dad looks for his teeth. In the next shot, Bob scolds the underwear while Dad comments on his grandma's pies. In the third shot, Bob wonders if it's the road to Tipperary while Dad calls for a kitty.
- In three shots, Jonah attempts to climb on his camel, but fails.
- The Pirates are discussing about Mr. Lunt's Aunt Lucy.
- The back of the pumpkin says "Slap me, I'm Irish."
- Larry and Mr. Lunt were looking for the ping-pong ball when Larry drops his telescope which hits Mr. Lunt.
- Khalil was explaining to Jonah about the Ninevites when he falls off the cliff.
- Jonah sat down and fell off the edge of the cliff, then emerges, having survived.