One of Toriel's sprites, a facial expression of her with an uneven frown and an eyebrow raised slightly higher than the other, is internally called "dreamworks", referencing the "DreamWorks Face", a nickname for a facial expression comprised of a confident, uneven smirk and one eyebrow being raised while the other is down. It is named as such for the film studio DreamWorks Animation, which frequently uses this facial expression in promotional artwork for its movies.

The Spoiler:Amalgamate enemies appear to take after an identically-named series of foes from The Halloween Hack, a 2008 ROM hack of EarthBound that Toby Fox made in high school; like the ones in Undertale, Spoiler:the Amalgamates in The Halloween Hack are comprised of multiple earlier enemies fused together.

Furthering the connection to the EarthBound fanbase, Spoiler:"Amalgam", the battle theme for most of Undertale's Amalgamates, is composed mostly of samples from the Cave of the Past and final boss themes in EarthBound, including the processed sample of the Beach Boys' 1970 song "Deirdre".

The tracks "Bonetrousle" and "Heartache" were originally composed for an early idea for Deltarune (whose gestation predated that of Undertale) before being repurposed here. "Bonetrousle" was initially the main battle theme for Deltarune before being replaced with "Rude Buster", while "Heartache" was originally titled "Joker Battle", implying that it was initially the battle theme for Spoiler:Jevil before being replaced with "THE WORLD REVOLVING".

The Japanese version of the game redubs Flowey's "That's a wonderful idea!" voice clip to a Japanese equivalent. In a DM sent on Twitter to VTuber Houshou Marine, Undertale creator Toby Fox confirmed that he voiced the Japanese line himself.

In the Xbox One and Xbox Series X/S versions of the game, the Dog Shrine is bulldozed and a Dog Casino is built in its place, containing a similar slot machine side quest that can unlock decorative items and 11 Xbox achievements. One of those unlockable items is a poker table featuring Sans, who can comment on your prizes found in the room. Spoiler:During a Pacifist run following the final boss fight, the player can return to the Dog Casino to find Mad Mew Mew in Sans' place, who will also comment on your prizes.

In the Nintendo Switch version of the game, the Dog Shrine from the PlayStation 4 and PlayStation Vita versions appears abandoned and in shambles. The only new addition is a red and blue door referencing the Switch's Red and Blue variant Joy Cons which are used to open it. The door can be opened Spoiler:following the Mettaton EX boss fight and allows players to access a boss fight exclusive to the Switch version, Mad Mew Mew. Spoiler:This character is implied to be the spirit of Mad Dummy after it possessed a "Mew Mew Kissy Cutie" doll belonging to Alphys.

In the PlayStation 4 and PlayStation Vita versions of the game, there is a secret area Spoiler:hidden underneath the sink in Sans & Papyrus' house called the Dog Shrine. Playing through the entire donation side-quest contained within, in which the player gradually gives enough gold to a Dog housed in a Japanese-style shrine, awards the player a total of 15 PSN trophies and numerous prizes the player can interact with in the room.

The song from the OST, "She's Playing Piano" by Toby Fox seems to be a rendition of the popular webcomic series Homestuck's "Doctor." Toby Fox would eventually make a scrapped remix of the song titled, "Patient," which was originally intended for Homestuck but was remixed into Undertale's "Another Medium."

The song "Hopes and Dreams" is comprised of various songs heard throught the game; some examples include "Snowdin Town" and "Your Best Friend".

The unused music track "mus_smile" is actually Muffet's laugh, but slowed down with its pitch lowered.

If you listen closely, the music played after getting a game over can be heard halfway through the song "ASGORE". Spoiler:This is fitting, as Asgore is the only main character in the true pacifist route that the player must kill.

In the neutral route, Spoiler:if Flowey closes your game after killing Asgore, when you load up your game again the save file's name will be changed to Floweytale.

When an enemy without a death sprite dies, it will use Aaron's death sprite as place-holder for any enemy without one.

The song "But Nobody Came" sped up 1600% sounds similar to another Undertale song, "Your Best Friend".

The character W.D. Gaster shares some visual similarities with the character Uboa from Yume Nikki, another RPG-based title. Their appearance is also similar to Dr. Andonuts from Undertale creator Toby Fox's Halloween Hack for EarthBound.

While meeting Sans for the first time, Spoiler:Sans will ask the protagonist to turn around and shake his hand, which has a whoopie cushion hidden in it. However, if you immediately exit the game without saving and then meet him again, he will ask you if you've heard his joke before, since the main protagonist turns around before being asked.

Spoiler:After beating the game by only killing Toriel, Asgore, Papyrus, Mettaton, and Undyne, Sans will call the player after the Omega Flowey fight to tell them that the annoying dog became president.

The track "Waterfall" almost exactly matches the melody of "Spear of Justice", but at about a third of the speed.

By speeding up the song "The Ruins", it is almost identical to the songs "NGAHHH!!" and "Spear of Justice".

The opera scene with Mettaton is likely a parody of "Aria di Mezzo Carattere" from Final Fantasy VI.