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.

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.

The emblem on Ralsei's robes went through two different renditions in early development. Initial concept art by Toby Fox depicts him with a fireball icon on his robe, matching a statement in an interview where he stated that "[he] was going to give a certain character a fire spell, but decided against it for the first chapter." Later pre-release concept art by Temmie Chang, meanwhile, depicts Ralsei's robes as bearing an upside-down spade symbol. Come the release of Chapter 1, and the design would eventually be changed to a heart; however, most of Ralsei's overworld sprites in Chapter 2 change this to the inverted spade design.

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.

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".

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 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.

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".

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.

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 popular 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.

One piece of concept art for Chapter 2 by Gigi DG, depicting the entrance to Queen's Mansion, features a note indicating that the design of the building is taken from "that toy story ride." This most likely refers to the Tokyo DisneySea version of Toy Story Mania, which similarly features a giant, grinning effigy of Woody's head as its entrance.

An early version of "THE HOLY" was posted on Toby Fox's personal website on July 12, 2015, over three years before it first appeared in Chapter 1 of Deltarune. This iteration of the track was titled "treasure_discovered.mp3", indicating that it was written with a more mundane purpose in mind compared to the released chapters, where it plays while standing before a Dark Fountain.

If the player talks to Noelle during the epilogue in Chapter 1, tells her about Susie eating chalk, and then imports the resultant data to Chapter 2, she'll gift her an entire lunchbox full of chalk during the prologue to the latter, complete with a unique cutscene.

When brought into the Dark World, the chalk turns into the LightCandy healing item; using it on Noelle results in her commenting on the fact that she'd previously given it to Susie.

Within the data for Chapter 2 are alternate graphics for the chapter's final cutscene, in which Spoiler:Kris creates a Dark Fountain within their living room. Most of these graphics go unused; one set is repurposed for the film that plays in the theater in Queen's mansion, showing Spoiler:the Knight creating a Dark Fountain, but it's cut off at the top.

In the background of Seam's shop, one can spot a doll designed after Yoki, a character from Deltarune designer Temmie Chang's games Escaped Chasm and Dweller's Empty Path. In Chapter 2, the Yoki doll is redesigned to match changes in Chang's own depiction of the character. The original design was initially still present in Chapter 1, but was later altered in the Version 1.08 update to match Chapter 2.

The DogDollar that Kris obtains from the Annoying Dog's alleyway in Cyber City contains unused dialogue for if the player attempts to use it, reading "(Where'd this come from?)". In normal gameplay, the DogDollar can't be selected like a typical item, making this text impossible to see without hacking.

In the original release of Chapter 2, Spoiler:the "WRECK", "PAUSE", and "SPEW" VCR icons that appear during Spamton NEO's ultimate attack only showed up during the hidden Weird Route, and thus were absent from his fight during the normal route. While this difference was initially interpreted by fans as an intentional artistic decision, in actuality it was the result of an oversight: Spoiler:the icons were coded to appear at certain coordinates relative to the room where Spamton NEO is encountered. Because the fight on the normal route moved Spamton NEO and the player far out of range, the icons were consequently left offscreen.

This error was eventually fixed in the v1.08 patch, with Spoiler:the icons appearing in the proper location on both routes instead of just one. The patch additionally adds a new smoke effect after Spoiler:Spamton NEO's ultimate attack ends on both routes.

Within the data for Chapter 2 are unused animations for both Lancer and Rouxls Kaard where they transform into their respective Light World forms (a Jack of Spades card and a rules card) when entering the player's inventory. In typical gameplay, the associated code for these animations is deactivated, with Lancer & Rouxls simply sliding into Kris' sprite.

The CHECK description for Spoiler:the Pipis enemies, which can only be encountered on the Weird Route, reads "Pipis - ''The Original'' An invasive species of freshwater clam." This appears to reference two real-world entities that Spoiler:are also called Pipis. The first portion of the description seems to nod to a restaurant in Puerto Vallarta, Mexico, which uses the tagline "The Original." The second portion, meanwhile, references a pair of edible saltwater clam species in Australia and New Zealand; the use of these clams as food is further referenced with Spoiler:Kris' "Fried Pipis" ACT during the Spamton NEO fight at the end of the Weird Route.

Within the data for Chapter 2 is an alternate, sped-up version of "Digital Roots" that lacks the ambient wind sounds. The existence of this track is a marked deviation from the rest of both Deltarune and Undertale, which otherwise speed up and slow down tracks in real time.

The filename for this unused variation is "spamton_house.ogg"; as "Digital Roots" itself uses the filename "spamton_basement.ogg", this seems to imply that the faster version was originally meant for Spamton's shop, which instead uses "Dialtone" (named Spoiler:"spamton_neo_after.ogg" in the game's files) in the final game.