In order to fit the TV length, some minor aspects of the stage show were cut: The original prologue of Patchy the Pirate crashing the show was replaced by an animated prologue of the SpongeBob characters about to watch the show using previously animated footage from the policy trailer, made in conjunction with ScreenVision Media, with some new lines dubbed in. The boulders from the volcano were initially represented by giant bouncy balls coming from Rube Goldberg devices from both sides of the stage, unfortunately, the theater could not accommodate said devices. The second reprise of "Bikini Bottom Day" at the beginning of act II was removed. Due to time, the beginning of the third verse of "Best Day Ever" was cut. In the original stage show, the SpongeBob theme song happened after the curtain call, but due to time, the theme song is sung right after the "Bikini Bottom Day" finale, followed by a proper curtain call.
Lilli Cooper does not reprise her role as Sandy since, at the time, she was performing in "Tootsie: The Musical" on Broadway.
Stephanie Hsu doesn't reprise her Broadway role as Karen the Computer, as she was filming for The Marvelous Mrs. Maisel during the time of shooting.
On October 17, 2019, it was announced that Nickelodeon would air a television special of the Broadway show titled The SpongeBob Musical: Live On Stage!, to be filmed in front of a live audience and feature members of the original Broadway cast such as Ethan Slater, Danny Skinner, and Gavin Lee. On November 19, 2019, it was announced that Tom Kenny would reprise his series role as Patchy the Pirate for the special and that it would air on December 7, 2019.
The star hand symbol that the anchovies do during "Super Sea Star Savior" was added to the choreography by ensemble members Lauralyn McClelland and Abby C. Smith. Both are alumni of Oklahoma City University, where the mascot is a star. The hand symbol is the same one used at the university, and they recommended adding it to the choreography.