The Venom Brigade, the game's antagonists, were originally moles as opposed to snakes. In addition to this, the fourth mole was yellow as opposed to Handy's blue coloration. The change from moles to snakes was done because Cruise Elroy wanted more distinction between the human Annalynn and the game's enemies.

Annalynn originally began development as Minecade, starring a generic male miner. After being inspired by Ms. Pac-Man, however, Cruise Elroy replaced him with Annalynn, with the game being renamed in her stead.

A spider enemy was originally set to appear if the player took too long in a level, but was cut since their mechanic would run contrary to the game's focus on enemy combos.

The spider, now named Gil, would appear in a 2023 remake of the 2016 version of Annalynn as an optional enemy.

The game's unlockable palettes and Practice Mode stemmed after Cruise Elroy added "perfect bonuses" to the game, as he wanted to give players more incentive to try to perfect every level. To this end, Practice Mode was added to avoid players having to replay the entire campaign from the start to reach a level they wanted to perfect.

Unused power-ups include an hourglass to slow down the Venom Brigade and a potion which would shrink them and render them harmless for a short time. They were scrapped due to being too similar to the final game's pickaxe powerup, but sprites for them were produced.

Icicles were planned to be a hazard in the Ice Grave area of the game, but they were cut as Cruise Elroy thought that the area's wind and ice physics were enough to make the area challenging. Sprites for the icicles were produced, however.

Some cut bonus items include a candle, diamond, emerald, and drill. However, the candle was reused for the 2016's mode bonus items.

During the development of the Nintendo Switch version, exclusive guest character Anton received a few scrapped sprites, including one with a closed mouth. A bottle of a red beverage and a red ball with eyebrows and a beard (presumably a reference to Antonball, Anton's debut appearance) were also planned to serve as Anton's life counter before being replaced with beets in the final release.

On August 16th, 2023, Cruise Elroy revealed that he usually sketches out concepts for Annalynn before implementing them in game. While many of the sketches shown are present in the final release, some unused concepts are also shown, such as an orange character named Annabelle (presumably a second player character) and Mappy-style trampolines.

Among these sketches is also Mike drawn with an expression mirroring that seen in the "Today I Will" meme.

Early development plans involved Annalynn being released as part of a 4-in-1 collection of arcade-style titles. The other games were dropped to focus on Annalynn.

The Mineshaft and High Score themes from the 2016 version of the game were remade for the 2021 release. While the Mineshaft theme is a near-identical conversion, the High Score theme is quite different.

As of version 1.3, after inputting a secret code on the Practice Mode select screen, "Mike%" is activated, which adds a timer to the game which stops once Mike is defeated. This is presumably a nod to the Mike% speedrunning category found on the game's page on Speedrun.com.

If this code is active while playing the game's final level, Mike is found sleeping in the corner of the boss room.