In an interview with TechRaptor, lead developer Ryan Koons stated that the decision to make HuniePop a gameplay-centric title instead of a story-centric one like other dating sims didn't happen until months into development. The original intention was to make a traditional dating sim, only for Koons – who already had little interest in storytelling in video games – to overhaul the concept due to his growing ennui.

In the same interview, Koons stated that he deliberately sought to avoid many of the cliches associated with dating sims, particularly "the usual innocent waifu style character types." Consequently, the game's cast are based on people from his own life, and the writing is much more irreverent than other dating sims. In particular, Koons described deuteragonist Kyu Sugardust as a raunchy fictionalization of her voice actress, Jaclyn Aimee.

Early in development, there was a planned dateable character known as "Jessica". This character was developed into the final game's character Tiffany.

The name was slightly altered and given to another dateable girl, Jessie.

The character Lola has a cut outfit featuring her in a peacoat and scarf. According to HuniePot, it was cut to make room for her bikini outfit.

The tokens for the game were originally square (rather than circular as seen in the final game) and also featured different icons.

The song for the "Lusties Nightclub" location went through several changes before release.

When first asked to make the music, composer "WorldofWandag" made a heavily dub-step inspired club song for Lusties Nightclub, but it was left out because he felt it was "too crazy for a club scene that involved cute anime girls."

The second version of the song is more close to the version found in the final, however it featured lyrics. "It [the song] was a 'Romanian' club song I composed for a feature film. They didn't end up using it so I took out the lyrics and figured it would be a great club theme for Huniepop. Luckily, it worked."

For the game to be released onto Steam, it had to be censored in order to abide with their restrictions on adult content in games.