This is the first Hollywood-studio animated film to use hand-drawn animation since Winnie the Pooh (2011), which also starred Tom Kenny.
Bob Esponja (1999) staff from seasons 1-3 returned to work for this movie, including creator Stephen Hillenburg. Hillenberg returned to the series full-time starting with Lost in Bikini Bottom/Tutor Sauce (2015). He first left the show after the first movie, although he still reviewed episodes and gave suggestions. It was announced by Paul Tibbitt in December 2014 that Hillenberg would work on its 10th season.
Bubbles the Magic Dolphin is completely made with stop-motion.
Squidward inking was originally supposed to be a common element of his character in the Bob Esponja (1999) show. However, the writers could not come up with a way to make it seem comical, so this was eventually scrapped.