The film follows the plot of the TV series VeggieTales, focusing in a big kitchen show of cucumbers, tomatoes, celery, peas, squashes, and carrots. It begins with a live action sequence of The Pirates Who Don't Do Anything, awaiting their treasure: tickets to The VeggieTales Movie. They sing the theme song, sail to the movie theater and sit in front-row seats to watch the film. In the movie proper, Bob the Tomato (voiced by Phil Vischer) and his best friend, Larry the Cucumber (voiced by Mike Nawrocki), say "hello" to the audience and tell them they are going for a visit to Larry's parents (both voiced by Bob West and Verna Felton) at their house because school is out. They ask the audience if they would like to come with them to see Junior Asparagus (voiced by Lisa Vischer) for a birthday party and a sleepover at his house. The audience agree to go. Then Bob and Larry finish packing their clothes, toothbrushes, stuffed animals, and snacks.
After eating breakfast in the dining room, Bob and Larry hear a vacation bus honk and run outside to see Jerry Gourd (also voiced by Phil Vischer) and his trusty pal, Jimmy Gourd (also voiced by Mike Nawrocki), arrive on time to drop them off at Larry's house in Anville. They are introduced to the audience and tell them they are invited to Junior's party "once and for all." Jerry says they'll be there Sunday afternoon as fast as they can. After this, Bob warns him and Jimmy that if they are not showing up to Anville, they will be marked off the inviting list. Larry, who is being nervous, is going to tell that he and Bob are going to need the audience's help today, trying to get ready for Junior's big surprise party and keeping it a secret because he has promised Bob not to tell Junior that they want the party to be a surprise. Bob and Larry get on the bus and enjoy their long ride to Anville.
Meanwhile, Jimmy and Jerry make their way to Anville and drop their friends off at Larry's house where his parents wait on the front porch. Larry's father brings them inside and gathers everybody in a circle to make arrangements for celebrating Junior's birthday at his house. Bob asks him what Junior's big surprise is going to be. Larry's mother happily says that it will be a special scrapbook with pictures of him over the past years (which will be a present for him). After the plan is made, Larry's mother tells her son to help make a birthday cake.
While wrapping presents for Junior, Larry's father tells Bob about when Junior was born in Townsville and how he was raised by his parents, Dad (voiced by Dan Anderson) and Lovey (voiced by Gail Bock), as their child, showing pictures of them in the book they made. Bob then replies "If this book is just a scrapbook, I'd rather call it a birthday photo album", which Larry's father accepts.
In the kitchen, however, Larry asks his mother what Junior's next age will be. Larry's mother admits that he is going to be eleven years old. Then she warns her son that if Junior knows about the birthday photo album, the surprise will be spoiled. Larry becomes concerned and needs to make sure they be quiet and not let Junior find out what they are doing.
After their chores for the party are completed, Larry's parents discover Archibald (also voiced by Phil Vischer) coming over to warn them about when all the money was stolen by a greedy pickpocket named Hector Polito (voiced by French Stewart). He also reveals that Polito is planning to take anything else he can find, including Junior's present, sabotage Anville and use the bank he has robbed as a hideout. This story upsets Larry who admits that Polito is actually a money wizard. Bob, not understanding that Polito doesn't want an allowance, finds out about him and learns from Archibald that he will aid two more thieves to search every house in the city to raise different things for a fee of $100 punctually (naming his robbery team "The Criminals").
Larry's parents suddenly realize that Polito doesn't know how to share things and that he will sell items to his hideout for a grocery sale if he wants to pay a $100 reward. Bob asks Larry if this means the party will be canceled after Polito steals Junior's present, which he reluctantly agrees. Archibald departs and makes them promise not to tell anybody else about Polito. Larry begins to think properly and finally comes up with a plan to repair the robbed bank, send all the money and items back to their owners, and teach Polito a lesson of what it is like to share.
During his sleepover, Larry wishes for a beautiful girlfriend to marry at the surprise party since it reminds him of when he was dancing with his sea lion doll, pretending her name is Barbara Manatee. Bob overhears this while sleeping in the living room and hopes Larry will have a "pure spirit" of his own.
Meanwhile, the next day, Polito lives in a deserted house near a river bank in Bangus Valley. He uses a stolen car television to spy on Larry's family and finds out what they are doing for Junior's birthday. In order to raise the cash reward and make his job very rich, Polito devises a scheme to rob every house by pilfering millions of stuff, sell them in his grocery sale without being responsible, and freeze Anville by turning the city into another part of the valley. And when his idea works out, then he will become a wizard to rule the world by exploding the valley and ruin the citizens' jobs by throwing the stolen money into a pool of molten iron (which will cause an avalanche).
After that, Polito realizes that he needs two more people to pose as bank criminals and help get his plan finished. The pickpocket drives his large rocket ship truck called "The Booster" to Maxville, where he meets a book collector named Lyle (voiced by Steven Weber) and his stepfather, Pepito (voiced by Dana Carvey), who has tried to find himself a career after he retired from work as a barber fourteen years ago. Polito then reveals to Pepito and Lyle about his plans for a grocery sale at his hideout, forcing them to become criminals and move to his mansion to help collect the reward, destroy the stolen money in a sack, and rule the world. On the ride back to Bangus Valley, however, Lyle tells Polito about when he collected books for a children's novel sale if he wants to pay $465 for himself.
Later, while helping Bob make birthday cards for Junior, Larry discovers that his wish has come true and meets a pretty 16-year-old female named Ella (voiced by Kat Cressida), who doesn't have a boyfriend. Ella introduces herself and asks Larry what they are doing today. Larry says that they are preparing for Junior's birthday party and keeping it a secret. Then his parents show Ella what Junior's surprise is and Larry learns from her that she once had a good-looking young friend named Joey seven days earlier. After Ella and Joey dated each other at News Café in Miami, they met Polito before and found out that all the money has been pilfered by him as a thief, which caused them to argue about it and go their separate ways.
Not interested in her stories, Bob refuses to be friends with Ella and concludes that Larry needs to believe in his own soul if he wants to marry her immediately. Larry tells him not to be rude to Ella, but Bob doesn't trust her and storms off alone. Larry thinks Bob is right and Ella asks him if he wants to date her, which he gladly accepts. After this, Ella blows a magic sparkly heart in Larry's face and takes him to eat lunch with her family while singing her beautiful short anthem: "I Love You With All My Soul".
When Ella brings Larry to her home, he meets her parents (both voiced by James Coburn and Glenn Close) and her old brother, Kurk (voiced by Tyler Williams), who reveal to him about Polito planning a house robbery in Anville and that he is actually a human, much to his surprise. They serve lunch at the table and begin to have a conversation. Ella tells Larry that she can help him and the others seek revenge on Polito, send all the money and items back to their owners, cancel the grocery sale, repair the burglarized bank, and make new friends with Polito's two criminals. And when she does so, then Ella will receive money to pay for a honeymoon with Larry after he marries her at Junior's party.
After lunch, Larry comes across a vacant bedroom and finds a note taped to the door, not knowing who it is from. Ella admits that the note is from her sister, Louise, saying that she died because she had a terrible pain in her leg. Larry is brokenhearted and persuades Ella to trust in her own pure soul. Ella happily agrees, vows to Larry that they will be in love forever, and sends him back home.
Larry goes into the house and tells his parents that Ella has chose to help them surrender Polito to the police and allow the Criminals to be their new friends and celebrate Junior's birthday. However, Bob doesn't quite understand the truth and is outraged that Junior will be very disappointed if Polito sells his present to his grocery sale. Then he overhears their plan to demolish Polito's cash reward, trick him into sending back the money and items, and fix up the bank.
Back at Bangus Valley, Polito and the Criminals place dynamites around the valley to transform it into a canyon with fire, empty the stream with a giant vacuum pipe by pouring it into a sizable barrel, and flood the gorge by dumping out the water.