According to an interview with Toby Fox conducted by Nintendo of Japan, Sweet, Cap'n, and K_K were originally meant to be a single character. However, when concept artist Nelnal sent in three potential designs, Fox ended up enjoying them all so much that he reworked the character into a trio.

In Chapter 2, two of the in-battle quotes the Virovirokun enemy can utter are "Happy new year 1997!" and "I've got a love letter for you." These are references to two infamous real-world computer worms: Happy99, which was one of the first computer viruses to be widely and rapidly disseminated by email, and ILOVEYOU, one of the most destructive computer viruses of all time.

If Kris is downed during the Sweet Cap'n Cakes fight before using the "Dance" ACT on each member of the trio at least once, the cutscene where Susie and Ralsei learn the S-Action and R-Action abilities plays prematurely, effectively allowing the player to complete the fight much quicker than intended. The dialogue in the cutscene is also altered to reflect this change in circumstance.

Within the game's data is an unused ACT associated with Spoiler:the Spamton NEO fight in Chapter 2, in which Susie throws Kris at Spoiler:Spamton NEO's wires to snap them, similarly to the fights against the Werewires and Spoiler:Queen & Berdly; this ACT even contains unique graphics not seen anywhere else in the game. In normal gameplay, Spoiler:Spamton NEO's wires are instead snapped automatically by selecting the "Snap" and "SnapAll" ACTs, without the need for action commands.

In Chapter 2, after Spoiler:Lancer petrifies from being incompatible with the Cyber World, the player can push the resulting statue left and right; pushing Spoiler:Lancer all the way over to the table on the left side of the room results in a plate of spaghetti and a napkin falling onto the table and on Spoiler:Lancer, who will bring up the message "(He seems to be well-taken care of)" when checked.

In the initial release of Chapter 1, the player could obtain a "Wrist Protector" item at the start of the Dark World if they manage to reach the area in under six minutes; the item allows the player to skip text by holding down the C key.

In the Chapter 1 & 2 release, the Wrist Protector is removed, and its functionality is permanently enabled from the outset, even before entering the Dark World in Chapter 1.

Taking the mechanical hum outside Hometown's bunker and speeding it up by 666% reveals that it's actually a heavily slowed-down version of "mus_smile", the audio track that plays when Spoiler:accessing the hidden Wingdings version of Entry Number Seventeen in Undertale.

The characters Ruddin, Hathy, Clover, Lancer, and King all took their designs from a series of playing card illustrations that Tumblr user Kantonytes published in 2012, the year Deltarune first started development. In a tweet posted shortly after Chapter 1's release, Toby Fox credited Kantonytes' work as a key inspiration for the game as a whole.

If the player hacks the game to make Kris equip the normally functionless BrokenSword item, they will gain the "Failure" ability, which is unique to this weapon (though it lacks any special effects).

Prior to Version 1.08, Chapter 2 contained unused data for Susie gaining a plushie of herself in her room should Kris give her Queen's gift during the party's reunion at the Cyber City carnival. Adding the Susie plushie back in and interacting with it results in unique dialogue between Susie and Ralsei commenting on it.

In a tweet posted off the heels of Chapter 2's release, graphic designer Temmie Chang showcased not only the sprite for the Susie plushie, but also sprites for a Ralsei plushie and a Noelle plushie, indicating that Queen's gift was originally planned to morph into the likeness of whoever the player decides to give it to. In normal gameplay, the only selectable character who opens the gift is Berdly, who finds a plushie of himself with nipples.

Version 1.08 fixed a glitch that prevented the Susie plushie from appearing in her room (the acid tunnel sequence resetting Flag 307 to Flag 1). However, the dialogue associated with it still does not appear when the plushie is checked. Save files that were patched after completing the acid tunnel are unaffected, requiring the player to erase the file and start over in order to encounter the plushie on it.

In the initial "SURVEY_PROGRAM" release of Chapter 1, the Librarby's computer lab entrance uses a single door; Chapter 2 however changes this to a set of double doors, with the accompanying sign being horizontally squished and moved to the left side of the doorframe. Several stray pixels in the Librarby interior are also cleaned off.

Because Chapter 2 takes place just one day after Chapter 1, the Chapter 1 & 2 release changes the Librarby interior in Chapter 1 to match that of Chapter 2.

Within the files for Chapter 1 is an usused dialogue chain that simply reads "Blaze it." before opening a prompt where the player must choose between "Blaze" and "Do Not Blaze"; both options do nothing. The dialogue has an ID number of 420, which combined with its contents references the famous stoner catchphrase "420 Blaze It."

Within the files for Chapter 1 is unused battle data, including graphics and text, for a fight against Ralsei. As the unused text includes mentions of the training dummy seen in the final game, this data suggests that the game's combat tutorial would've originally seen Ralsei partner with the dummy instead of with Kris.

During the vessel creation sequence at the start of Chapter 1, if the player gives their creation and themselves the same name, the in-game narration will respond with a passive-aggressive comment about how on-the nose that is.

Within the data for Chapter 2 are an unused series of voice grunts; the filenames for them are all "Snd_txtrx" followed by a number. This name deciphers as "Sound Text Rx," implying that these files were intended for Rouxls Kaard, who during regular gameplay is one of the only characters to feature dialogue portraits but no voice grunts (instead using the generic text scrolling sound).

If the player Spoiler:downloads Spamton onto the EmptyDisk and attempts to use the resultant Spoiler:LoadedDisk item on the purchasable mannequin in Cyber City, a text box will appear stating that the item "squirmed and won't fit." This Easter egg appears to foreshadow Spoiler:the actual purpose of the LoadedDisk, which Spamton uses to become Spamton NEO by uploading himself to the discarded robot in the mansion basement.

While exploring Cyber City with Noelle in Chapter 2, the player can encounter a hidden alleyway marked with dog signs. Going down this path results in Kris being run over and downed by the Annoying Dog, only for the Undertale game over screen to appear in place of the standard one. The Annoying Dog proceeds to run over that too, after which Kris and Noelle wake up beside a dumpster with a Dog Dollar added to the player's inventory.

This Easter egg nods back to a Tweet posted by Toby Fox in 2019, which consisted solely of the Annoying Dog's car sprite with the caption "this is the last thing you see before you die."

Ambyu-Lance's recruit bio ends with the line "It's not down with the sickness." This plays off the title of the 2000 song "Down with the Sickness" by American nu-metal band Disturbed.

During the Spoiler:Giga Queen fight at the end of Chapter 2, if the player manages to avoid taking any damage during rounds one and two, Spoiler:Giga Queen will become enveloped with a blue aura during round three, and her attacks will become more aggressive and harder to avoid. To compensate, however, her defense is reduced.

In Chapter 2, if the player activates the Warp Door in Queen's mansion and uses it to revisit Cyber City, they will find one of the paths blocked off by an oversized toilet sprite. According to a tweet posted by Toby Fox during Chapter 2's development, the sprite was created at his request by the game's primary graphic designer Temmie Chang, only to end up absurdly large due to a miscommunication.

Furthermore, interacting with the toilet produces the message "(For some strange reason, a giant toilet-shaped toilet is blocking the way.)" This is a reference to the Iron Pencil statues in EarthBound, which produce the near-identical message "(For some weird reason, a pencil-shaped iron statue is blocking the path.)" when checked.