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A supermarket called Shopwell’s is filled with anthropomorphic grocery items that worship the human shoppers as gods who take groceries to the “Great Beyond” when they are purchased. Among the groceries in the store is a sausage named Frank, who has dreams of living with his hot dog bun girlfriend, Brenda, in the Great Beyond, where they can finally consummate their relationship.

After Frank and Brenda’s packages are chosen by a woman named Camille Toh to leave Shopwell’s, a returned jar of Bickle’s honey mustard tries to warn the disbelieving groceries that the Great Beyond is a lie. Nobody listens except for Frank. Honey Mustard calls on Frank to seek out a bottle of liquor named Firewater, before committing suicide. This creates an accidental cart collision that causes Frank, Brenda, and several groceries to fall out, including a douche who gets his nozzle bent, and plots revenge against Frank and Brenda.
Seeking to verify Honey Mustard’s warning, Frank leads Brenda, Lavash (Armenian national bread) and a bagel named Sammy Bagel Jr. to the store’s liquor aisle under the guise of taking a shortcut to their proper aisles. There, he smokes weed and learns from Firewater that he and other non-perishable foods invented the story of the Great Beyond as a noble lie to assuage past food’s fears of being eaten by shoppers. Frank, vowing to reveal the truth to the groceries, is encouraged to travel beyond the store’s freezer section to find proof. While waiting for Frank, Brenda and the others are led into the Mexican aisle, where they meet Teresa, a taco who falls in love with Brenda on sight.
Meanwhile, Frank’s friends Carl and Barry are horrified as they witness the other purchased foods being cooked and eaten by Camille, shown from the foods' perspective as brutal murder. Carl and Barry attempt to escape out a window, but Carl is killed when Camille slices him with a knife. Barry manages to escape and stumbles across a human druggie, who becomes able to communicate with his groceries after he injects himself with bath salts. After sobering up and attempting to cook Barry, the druggie is decapitated in a domestic accident.
Back at Shopwell’s, Frank reunites with his friends and tries to get them to come with him into the dark aisle but Brenda refuses and she and Frank end up having an argument until she, Teresa, Sammy and Lavash head back to their aisles, leaving Frank to head into the dark aisle solo. Once Frank reaches the dark aisle, he discovers a cookbook and finds pictures of humans eating food. Frank then rips out a few pages and sets out to reveal the truth to the groceries. Frank reveals the groceries pictures of humans eating food from the cookbook and they begin to panic. However, they choose not to believe him, fearing they lose their sense of purpose, prompting Frank to lash out at them for their blind belief. Frank then tries to rescue Brenda from being taken away but a women grabs her new package and Frank tries to find her, but loses track of her and gives up hope until Barry and other groceries from the druggie’s home return to the store with the druggie’s severed head, revealing that the humans can be killed. The groceries are able to drug the human shoppers and employees using toothpicks laced with bath salts. After saving Brenda from getting purchased, Frank apologizes to the foods for misjudging their beliefs and convinces them to fight against the shoppers when they start attacking them, and a store-wide battle ensues.
Douche, after absorbing the contents of liquor bottles, becomes a wild monster and takes control of the store manager named Darren by inserting himself into Darren’s anus and yanking on his scrotum to puppeteer his actions. Once he and Darren catch Frank, Douche gets revenge by biting on Frank’s torso. Barry and the other foods launch a rocket at Douche and Darren made from propane tanks and a garbage bin used to dispose of expired foods. Brenda rescues Frank from Douche and Darren just as the rocket hits them, sending them both through the store’s ceiling and killing them in an explosion. With the battle over, the foods celebrate their victory in a massive orgy.
Afterwards, Frank, Brenda, Barry, Kareem, Sammy and Teresa meet with Firewater and Gum, who have had a psychedelic experience and discovered that their world is not real, and they are merely cartoons voiced by famous actors in another dimension. Gum has constructed a portal to this dimension, and the groceries decide to travel there to meet their creators.