There are two allusions to the brony fandom: Twilight Sparkle calls Cadance her "pegasister-in-law," and Cadance says that her destiny was to lead other ponies with "True Love and Tolerance."[dubious – discuss]
The author description for A.K. Yearling reveals that she wrote an essay named "What Was The Name Of That Griffon Again? Or, Beak and Roaming Studies Recalled", which was published by the University of Equexeter's journal, Pegasus. This alludes to a similar sounding essay that J.K. Rowling wrote for Exeter's journal Pegasus in 1988, named "What Was The Name Of That Nymph Again? Or, Greek and Roman Studies Recalled".
Marapore is a play on Mayapore from the Indiana Jones franchise.
Two of the villages at the base of Mount Vehoovius are called Ponypeii, a reference to Pompeii, and Lusitano, a reference to the Lusitano breed of horse.
The story shares numerous similarities with the film Indiana Jones and the Last Crusade, such as the main character's search for a missing family member, an ally that later turns out to be an enemy, and a priceless treasure being hidden in plain sight among various fake or misleading treasures.
Flim and Flam introduce themselves as Farnum and Failey, a reference to Barnum and Bailey, two circus personalities who, along with Ringling Bros., created the famous circus, The Greatest Show on Earth.
The title of chapter 2, "Just a Frog and Bunny Show", is a play on the term dog and pony show.
One of the rabbits in Flim and Flam's show is named Foo Foo and uses field mice in its routine; this is a reference to the poem Little Bunny Foo Foo.
The title of chapter 4, "Taking Flock", is a play on the phrase "taking stock" which means to assess a situation.
The title of chapter 5, "The Warm, Fuzzy Truth", is a play on the expression "the cold, hard truth."
One of the ponies thinks that Fluttershy, when dressed as a shepherd, is acting as Little Pony Peep, a reference to the nursery rhyme, Little Bo Peep.
Twilight mentions Trotland and Bales, parodies of Scotland and Wales.
Applejack's last line, "That'll do, Fluttershy. That'll do." is a reference to the line "That'll do, pig. That'll do." from the book The Sheep-Pig or Babe, the Gallant Pig as it is known in the United States, and its film adaptation, Babe.
The country of Monacolt is a reference to the country of Monaco.
The part where Celestia asks her students to tear up their essays is a reference to the late Robin Williams telling his students to tear out the introduction of their textbooks in the film Dead Poets Society.
Rainy Air says, "I like raindrops on roses. But that's more a favorite thing than a fun thing." This is a reference to a lyric from "My Favorite Things" from the Rodgers and Hammerstein musical The Sound of Music.
In chapter 5, the Cutie Mark Crusaders ask the Mane Six if they are playing Monopony or Settlers of Canterlot, but Pinkie responds they are playing Whisk. These are parodies of the board games Monopoly, Settlers of Catan, and Risk respectively.
The title of chapter 8, "Dreamwalking in a Winter Wonderland", is a reference to lyrics in the 1934 Christmas song "Winter Wonderland".
In chapter 10, Apple Bloom references the "Deal with it" meme when she puts on a pair of moonglasses and says this phrase.
In chapter 13, Rarity mentions the department store chain Bloomingtail's, a play on the real-life department store chain Bloomingdale's.
Many of the agents working for S.M.I.L.E. are named after the NATO phonetic alphabet, such as Alpha Hoof, Bravo, Foxtrot, and Tango.
Chapter 7 is titled "Mares in Black", a reference to the popular UFO conspiracy theory about "Men in black", which, in turn, inspired a successful comic and film franchise of the same name.
The Saddle Hawkins dance is a parody of the Sadie Hawkins dance, in which girls ask boys to the dance. The tradition originated in the comic strip Li'l Abner.
Chapter 12 is titled " It's Element-ary, Dear Bon Bon", a reference to the phrase "Elementary, my dear Watson", often attributed to, but never actually said by, Sherlock Holmes. (Even though he never says it in the novels, he says it in the film adaptations starring Basil Rathbone.)
In chapter 2, Rarity makes a dress for Sapphire Shores to wear to the Glammy Awards, a reference to the real-life Grammy Awards.
Chapter 8 is titled "Follow the Yellow Trick Road", a reference to the song "Follow the Yellow Brick Road" sung by the munchkins in The Wizard of Oz.
Chapter 11 is titled "Cloak and Swagger", a reference to the term cloak and dagger, used to refer to situations or events that involve spying, secrecy, intrigue and mystery. It is also the title to a 1984 spy-thriller film.