The credits include the line, "This movie filmed entirely on location in a mall in Lombard, Illinois." The mall is Yorktown Center, former home of Big Idea Productions.
The creators originally thought of doing the story of Noah's Ark for this movie but animal fur would have been expensive to create. They decided on the story of Jonah since whales don't have any fur.
The voicing and singing for the 3 main messengers that came to Jonah inside of the whale, were done by the Gospel singing group Anointed.
Khalil is one of the few characters in a Veggie Tales feature to have limbs. (Due to the fact that he was not a vegetable)
After production wrapped up on this film, Big Idea was going to make another film called "The Bob and Larry Movie". It would've explored the origins of how Bob and Larry met and how they started VeggieTales. The film would've also featured human characters and would've shown how vegetables and fruits can talk. Unfortunately, Big Idea's bankruptcy and buyout from Classic Media forced the film into cancellation. Phil Vischer stated in his autobiography that while Jonah was Big Idea's "The Ten Commandments", The Bob and Larry Movie would've been their "Toy Story".