Howard R. Cohen learned from Charles B. Griffith that when the film was being edited, "there was a point where two scenes would not cut together. It was just a visual jolt, and it didn't work. And they needed something to bridge that moment. They found, in the editing room, a nice shot of the moon, they cut it in, and it worked. Twenty years go by. I'm at the studio one day. Chuck comes running up to me and says, 'You've got to see this!' It was a magazine article--eight pages on the symbolism of the moon in La Petite Boutique des horreurs (1960)."
The film was shot on a budget of $22,500 to $28,000 (nearly $300,000 in 2024), with interiors being shot about two days, utilizing sets that had been left standing from Un baquet de sang (1959).
When asked where he got the plant, Seymour replies that the seeds were obtained from a Japanese gardener who found the bulb in a "plantation next to a cranberry farm." This joke is lost on modern audiences. In 1959, it was announced that cranberry crops were tainted with traces of the herbicide aminotriazole, and, as a result, cranberry sales plummeted. In the stage musical adaptation, the plant's origin was changed to being an alien hybrid between a Venus flytrap and an avocado, which went over better with the audience.
At the time of shooting, Jack Nicholson had appeared in two films, and had worked with Roger Corman as the lead in The Cry Baby Killer (1958). According to Nicholson, "I went in to the shoot knowing I had to be very quirky because Roger originally hadn't wanted me. In other words, I couldn't play it straight. So I just did a lot of weird shit that I thought would make it funny."