In the livestreamed playthrough of Chapter 1 conducted for Undertale's sixth anniversary, it was revealed that Lancer's childlike characterization was originally far more subdued. Toby Fox later chose to exaggerate these elements after playtesters instead assumed that Lancer was a Danny DeVito-esque adult.

Rouxls Kaard's line "Lost...? Frightened...? Confused...? GOOD!! HA HA HA!!!" appears to be a reference to the 1995 edutainment title I.M. Meen, in which the eponymous antagonist says a similar line.

Catti and Catty's dad in Deltarune is a reference to Mr. Dink, a character from the Nickelodeon/Disney cartoon Doug. He mentions a character named "Douglas" (the name Dink would refer to Doug by in the series) and is seen next to a broken grill, referencing a scene from the original Nickelodeon run of the series where Doug imagines Mr. Dink turning into a monster in rage after finding out Doug broke his grill.

After completing the light puzzles, Berdly will accuse Susie of cheating, akin to when she "wavedash[es]". This is a nod to the exploit that originated in Super Smash Bros. Melee. It's fitting that Berdly says this, as his Dark World design resembles a mix of Fox McCloud and Falco Lombardi from the Star Fox series, who are two of the most popular characters used in the competitive scene for Super Smash Bros. Melee.

When speaking to Toriel at the end of Chapter 1, she'll mention how Asriel loved playing as the "green, egg laying lizard" from the game "Super Smashing Fighters," a reference to Yoshi in Super Smash Bros.

Toriel will also mention a related incident in which Asgore painted green spots on eggs as part of a birthday party for Asriel themed around the lizard (referencing Yoshi's eggs). The following morning, Asgore cooked the eggs for breakfast, which upset Asriel enough that it caused him to hate the book about "eating green eggs". This is a nod to the Dr. Seuss book "Green Eggs & Ham".

When speaking to Father Alvin about Asriel near the end of Chapter 2, he will mention about how Asriel used to beg for forgiveness for "dropping the lizard in the pit to jump high" in a video game. This is a nod to an exploit often used in Mario games, starting with Super Mario World, in which the player can jump off of Yoshi into a bottomless pit in order to land safely on a platform that they missed.

One of Mauswheel's battle dialogue is "(Rolling around at the speed of mouse...)". This is a reference to "Rolling around at the speed of sound", the opening line of the song "Escape from the City" in Sonic Adventure 2.

When looking into one of the grocery baskets filled with fruit in Sans' grocery store, it states that it contains "(Grapes, melons, oranges, and the scent of fresh pineapples...)". This references the DK Rap from Donkey Kong 64, specifically the outro line "walnuts, peanuts, pineapples smells, grapes, melons, oranges, and coconut shells".

After Queen realizes that she didn't capture Ralsei out of all of the Lightners due to not having enough cages, the sound effect that plays with the Iris Out zooming in on her face is the same sound effect used on the Iris Out on Mario when completing a level in Super Mario World.

In Volume 5 of his Famitsu column "Toby's Secret Base", creator and director Toby Fox revealed that Ralsei's name came from a period in elementary school where he and his brothers constantly experimented with RPG Maker, having long had a shared interest in game development. Fox's oldest brother spent years working on a game called New Genesis, which featured a protagonist named Ralse; Fox simply appended an "i" to the name when incorporating it into Deltarune years later.

In the same column, Fox stated that the prolonged development of New Genesis discouraged him from making games for a long time. When he finally returned to the field in his teenage years, he sought to temper his expectations from the outset by making smaller-scale titles and preemptively planning out his approach to development to avoid biting off more than he could chew.

In 2012, Toby Fox posted several Yume Nikki fan songs to his Tumblr account. One of these, "waltz of seccom masada" (named after a fan nickname for the piano-playing NPC in the spaceship area), bears strong similarities to the Deltarune track "Man" (heard in the hidden rooms where Kris can obtain an egg from an invisible NPC behind a tree), indicating that Fox repurposed and rearranged the song for his own project years later.

Although Chapter 1 was given a surprise release in 2018, with Toby Fox giving no prior public indications of its existence, Deltarune had been teased in secret since at least 2015. Three months after Undertale released, the fan site DeltaRune.com announced that it would be rebranding to Dreemurr.com at Fox's request; Fox didn't tell the owners of Dreemurr.com why he didn't want them to use the domain. However, after the fan site fulfilled his request, Fox used deltarune.com to host an image called him.png, a passage of Wingdings text only readable by turning up the brightness using image editing software.

While the text initially parroted the phrase "THIS NEXT (space) EXPERIMENT (space) SEEMS (space) VERY (space) VERY (space) INTERESTING" from the unused room_gaster event in Undertale, by July 1, 2016, the text was edited to read "THREE HEROES APPEARED (space) AT WORLD'S EDGE", later being edited again by August 17 to say "THREE HEROES APPEARED (space) TO BANISH THE ANGELS HEAVEN". Both revisions quote portions of the legend that Ralsei recounts in Chapter 1, indicating that these parts of the game's backstory were already conceived by this point.

Following the release of Chapter 1, deltarune.com would be refurbished as the official website for Deltarune itself. Consequently, earlier versions of the site only survive through snapshots on the Wayback Machine, a URL archiving platform hosted by the Internet Archive.

In an interview that Toby Fox conducted with the Chapter 2 development team, Taxiderby, one of the game's programmers, stated that the Spamton cherub that appears when pressing F1 during the Spamton and Spoiler:Spamton NEO fights was a spur-of-the-moment suggestion. According to them, Spamton's line "[Press F1 For] HELP" was already written, but it was originally a meaningless non-sequitur. After Fox suggested the idea of giving F1 an actual function in the fight, Taxiderby came up with the Final Fantasy-inspired Easter egg, putting it in singlehandedly after Fox gave his approval for the idea. In the same interview, they stated that they were surprised by its popularity, having made it purely as a throwaway gag.

In the September 14, 2023 edition of the Undertale/Deltarune newsletter, Toby Fox revealed that a stealth sequence was planned for Chapter 3, only to be cut partway through development due to his dissatisfaction with it, stating that "a mechanic which basically just makes you move slower isn't necessarily fun." To compensate for the segment's removal, Fox included an MP3 file of the music that was composed for it, as the song would not be featured in the final game.

In the Undertale sixth anniversary livestream, Toby Fox stated that the scene in Chapter 1 where Susie holds off from attacking Kris due to her respect for Toriel was inspired by a real encounter with a bully that he had. According to Fox, the bully knew his mother and stated that they would've beaten him up if she wasn't nice to them.

In Chapter 2, when Queen challenges Kris to an arcade match, the arcade cabinet presented is so large that Kris is unable to reach the controls. While the released game conveys this solely through narration, its internal data contains an unused animation depicting Kris reaching up towards the cabinet's joysticks. It is unknown why this was removed, given that it fulfills the same function as the textual description.

After Kris exits the bathroom during Chapter 2's epilogue, the interior of the Dreemurr household noticeably changes: the phone and the painting by the trash can are both moved further up the wall, and the refrigerator grows noticeably taller.

These changes are also present in a mockup of the interior found in the game's files. However, the mockup is set during the day instead of at night, and the painting beside Toriel's chair is moved upward. This implies that the nighttime version of the interior was based on the mockup (with only minor touch-ups) without cross-referencing the layout seen earlier in the game.

In a tweet made a few months after Chapter 2's release, development staff member Samanthuel Gillson shared an early sprite sheet of Hacker featuring a considerably different design compared to the final game, depicting his body as the shaft of a pointer icon rather than making the entire symbol his head. While these were ultimately done away with after Hacker's design was revised, one sprite depicting him pointing forward is still present in the game's code.

Of note is that Hacker's head turning into a click icon is present in the sprite sheet in Gillson's tweet, indicating that this component of Spamton's sidequest (in which the click icon indicates an area that Kris must check in order to access the mansion basement) was already conceived by this point. Consequently, it is unknown what the leftover pointing sprite was made for.

Within the data for Chapter 2 is a placeholder graphic for Queen's arcade cabinet that depicts it with green paneling and the word "Xbox" crudely written on the marquee. Despite the fact that it was never intended to be featured in the normal course of play, the sprite was altered in the version 1.06 update to remove the "XBOX" text, presumably to avoid potential trademark issues.

In Spoiler:the Weird Route version of Chapter 4, one pivotal scene depicts Spoiler:Kris, possessed by the SOUL, forcing Noelle to re-don the Thorn Ring from Chapter 2 by slowly creeping towards her as she backs away in fear across a couch. In the original release of the chapter, this gives way to an animation Spoiler:of a rose blooming and then crumbling against a black screen, located in the same place as Noelle's sprite. In the Version 1.01A update, this was replaced by Spoiler:a single red pixel, possibly as a placeholder graphic, which in turn was replaced in Version 1.01C with another animation depicting cracking red glass. The original animation is outright removed from the game's files in these later updates rather than being merely disabled.

The reason for this alteration was not explained in the official changelogs, which respectively described the changes as a "Small graphical alteration to a certain scene" and "Strengthened imagery while maintaining a scene's intended meaning". The original animation was likely changed in response to complaints from players who interpreted it as Spoiler:Noelle being forcibly "deflowered" (taking her virginity, in this case through rape) literally, in addition to being driven insane, and to counter-complaints Spoiler:lamenting the reduced emotional impact when the single red pixel was implemented. Spoiler:The couch sequence moments prior remained unchanged with each update, making it unknown if Spoiler:the rape implication was intended, presumably metaphorically, in all versions of the scene.