A countless many fanfics have referenced Cupcakes due to its infamy.
- Better Living Through Science and Ponies: GLaDOS tries to convince Pinkie Pie that her friends know she is just a couple steps away from becoming a serial killer and baking them into cupcakes.
- Turnabout Storm: While Phoenix and Pinkie Pie are examining the victim's room, the inevitable ladder versus step ladder Running Gag is brought up. Phoenix compares it to cupcakes and muffins, Pinkie compares it to hacksaws and saws. The whole scene can be considered a Big-Lipped Alligator Moment.
- Hoofstuck: In order to enter the Medium, Pinkie Pie needs to destroy her cruxite artifact, shaped like Rainbow Dash, with a knife. Unlike here, though, she does not savor the idea of carving up Dashie.
- Sonic Generations: Friendship Is Timeless : Discord straps Rainbow Dash into a table that "looked like it was straight out of a horror story".
- Ed, Edd n' Pony
: Chapter 2 reveals Ed is a brony, thanks to Sarah. Chapter 2 also reveals Ed was unfortunate enough to read Cupcakes. What does he do next? He pounds his head against the cement floor to get it out of his head. The others brush it off as just Ed being Ed. A later chapter has Ed checking to see if Rainbow Dash was okay before eating a cupcake. - The Party Never Ended has it appear as a nightmare Pinkie Pie is trapped in at one point.
- Progress: While in Pinkie Pie's apartment, Princess Luna watched a gut-wrenchingly bad and graphic cable television horror film version of Cupcakes while Pinkie was busy in the kitchen. Luna was then startled by a completely (well, mostly) innocent Pinkie, and became temporarily phobic of pastries and the color pink. She tore the room apart before fleeing, but was forgiven, got over it quickly, and enjoyed Pinkie Pie's company later the same day.
- World Of Ponycraft: Pinkie interrogates a cultist by telling her a cupcake recipe she read in a fanfic once.
- Silent Ponyville uses this fic as one of Pinkie's nightmares, even having her turn into this incarnation of Pinkie in one of the bad endings.
- In My Little Denarians, the denarians briefly turn Pinkie into her Cupcakes version by tampering with the script, forcing Harry to invest a bit of his soul into giving her free will.
- Rainbow Leap uses... well, almost all of these as parallel universes.
- Pony POV Series:
- The series' version of Pinkie Pie tells the readers to stop talking about that "stupid fanfic" when she gets to a point in her introduction where she mentions cupcakes. The scary part is she nearly gets taken over by Angry Pie, who is arguably every bit as psychotic as the Cupcakes version. This version of Pinkie really hates this fic. In one chapter, the cast gets trapped in Princess Gaia's Lotus-Eater Machine. What is part of Pinkie Pie's fantasy is all copies of this fanfic being burned and a computer virus purging it from the internet.
- Pony POV Series Chaos Verse: Cupcakes is reenacted by Discord to entertain his daughter and her friends. It is recreated as a live action show with most of the flaws of the infamous live action show of My Little Pony, turning Cupcakes into a comedy that makes Chaos!Pinkie Pie and Fluttercruel laugh for 10 minutes.
- Getting Back on Your Hooves has Pinkie say she does not make cupcakes where people can see, and mentioning suing someone for defamation of character.
- Super Filly Adventure has several references to it, such as Pinkie asking player character Jade if she wants to make cupcakes with her, Twilight referring to a book called 'Cupcakes' (which Jade insists she should not read), and Pinkie musing on the purpose of a 'hacksaw' and claiming she is seen an 'evil' version of herself in the mirror.
- EarthBound (1994) romhack EquestriaBound has cupcakes as healing items. Their description includes the following: "100% not made of anything questionable".
- Po-Ni-Oh: The Abridged Series (a ponyfication of Yu-Gi-Oh! The Abridged Series) has a shout-out during the soap opera parody in episode 7, where Grandpa shooting Tristan becomes Granny Smith making Derpy into Cupcakes (With Cupcakes capitalized to drive the point home).
- A Series of Stories, an Affectionate Parody that pokes fun at the various cliches of the fandom, references this story after Rainbow Dash pretends to be her Rainbow Factory self (the premise is a horror novel in this universe) as a prank on Twilight, pointing out her doing something like that would be as outrageous as 'that horror novel Pinkie Pie wrote.'
- The Legend of Spyro: A New Dawn has Delilah mention the "Cupcakes Incident" on more than one occasion, which involved this universe and left her deathly afraid of cupcakes. Apparently, she at least witnessed at least some of the events of the fanfic itself. It did not seem to hurt her relationship with the canon version of Pinkie Pie though, who she lists as one of her best friends and is even upset she missed her birthday party. Though in the A New Dawn Side Story, Delilah is seen taking therapy for it.
- The Katawa Shoujo fanfic Hanako Bakes Cupcakes has Hanako brutally slaying Lilly, Hisao, Shizune and Misha after serving pieces of her flesh to them in cupcakes.
- Being Human A Portal Fanfic has GLaDOS claiming to Wheatley she wrote Cupcakes. She says it was very well received.
- My Little Caboose: Blue is Magic!: Tucker has a nightmare about him and Rainbow Dash being processed into cupcake batter by Pinkie and Caboose.
- Sweetie's Mansion: The intermission chapter mentions a novel about a seemingly cheerful girl who lures her best friend into the basement and murders her.
- The Pokémon adoptables website Global Pokédex Plus features a collectable item called the Suspicious Cupcake, an ordinary-looking cupcake with pink frosting.Description: Said to be baked by a mad Ponyta, if that's actually possible. You swear it tastes like meat...
- Ask Serious Rainbow intended to have Serious be a Rainbow Dash (technically a Rainbow Flash) who had been killed by a Cupcakes!Pinkie, but the person behind the blog changed their mind and had Serious killed by their Twilight, a la Pages Of Harmony. Pinkie had actually mercy killed Serious.
- The password to the unlockme.pdf included in the romhacking.net version of Final Fantasy VI Brave New World is named after the fic.
