Atari wanted Bubsy in: the Purrfect Collection to go by the shortened title of Bubsy: the Purrfect Collection, but producer Audi Sordie insisted that the title must include "in:" due to the original era of Bubsy games using "in" whenever a game had a subtitle, including Bubsy 3D's full title "Bubsy is 3D in Furbitten Planet". Development director Joe Modzeleski had a differing choice for the title, "Bubsy's Mew-sium for Mediocre Video Game Products", which he "pushed for for a while", but Sordie pushed back against. A joke working title for the game was "Bubsy Meets O.J. Simpson".

The box scan of Yamaneko Bubsy no Daibōken (the Japanese version of Bubsy in: Claws Encounters of the Furred Kind) included in Bubsy in: the Purrfect Collection is taken from project lead Audi Sordie's personal collection. According to Sordie, he worked in Japan for a period of time and once brought his partner over. Knowing that he loved the Bubsy series, she sought out a copy of the game while there and bought it for him as an expensive gift.

On the Meowseum selection screen, a text bubble can appear for a few seconds above a silhouetted Bubsy that says "Art's cool ;^)" in Comic Sans, a reference to the text bubbles from the ironic fangame Bubsy 3D: Bubsy Visits the James Turrell Retrospective. According to Limited Run Games lead Josh Fairhurst, there were discussions about including the fangame in the compilation, but they did not go through, likely due to the use of copyrighted and trademarked assets (such as the Applebee's logo, a Nokia ringtone, and the works of the real-life sculptor James Turrell), as well as potential age rating issues with the game's frightening imagery.

Bubsy in: the Purrfect Collection was produced by self-proclaimed "Bubsy World Heavyweight Champion" Audi Sorlie (who also worked on another tribute to maligned 1990s platformers, Arzette: The Jewel of Faramore). Sorlie claims that, growing up shy and quiet, he gravitated towards Bubsy for being "outgoing, extroverted, [and] exciting". He had previously done a documentary video on the Bubsy franchise for the Digital Foundry YouTube channel, the overwhelmingly positive response of which he claimed was a major factor in preventing him from committing suicide. Sorlie and Atari, the current license holders of Bubsy, wanted the compilation to be "sincere, fun, and personal", as opposed to the self-deprecation that had defined the Bubsy franchise during its previous ownership by Tommo Inc., stating:

On June 9, 2022, a fan animation was uploaded to YouTube by FlippinDingDong, depicting a tape recording of a fictional 1990s Saturday morning cartoon series based on the Gex franchise, framed as airing on the now-defunct TV channel Toon Disney. The video reuses Gex's one-liners and music from the original games. The animation went viral and FlippinDingDong would later be commissioned by Square Enix to animate the reveal trailer for Gex Trilogy. The trailer appears to play off of speculation that was spreading at the time about a GoldenEye 007 re-release, bait-and-switching the viewer into believing it would be a James Bond game before revealing Gex, who also has a spy theme, though the trailer would release after a GoldenEye 007 re-release was confirmed.

Later, a trailer would be released for Bubsy in: the Purrfect Collection that was also animated by FlippinDingDong. This trailer reused assets from the first trailer, including music and sound effects from the Gex games, as a double bait-and-switch, owing to Bubsy and Gex commonly being associated with one another on the internet (despite Bubsy games not having James Bond-inspired imagery).