- The original opening credits (up until episode 19) were visually inspired by Brooklyn Nine-Nine.
- The Bird's odd speech patterns (talking too slowly, saying "Hello" too often) are modeled after early episodes of Home Movies.
- Princess Celestia's voice is based on the Monarch.
- Rarity is indirectly based on Korra's mom. Getschman originally wanted to make a The Legend of Korra abridged series, but that fell through. So he took the jokes he already had planned for Korra's mom (the voice and the obsession with spaghetti noodles) and applied them to Rarity.
- Fluttershy appears to be singing (badly) the Doctor Who theme music.
- The Bird makes a joking reference to Monty Python and the Holy Grail.
- During the bunny stampede, a background pony can be heard frantically calling for a Holy Hand Grenade, another Holy Grail reference.
- Fluttershy believes one of the stampeding bunnies might be General Woundwort.
- The cows hail from a mystical land known as "The Far Side".
- Gilda has the voice of Mr. Plinkett.
- Celestia responds to her tidal wave of abusive mail with, "I will look for you. I will find you. And I will kill you."
- After an exasperating argument with Trixie, Twilight sarcastically asks her "Are you not left-hooved?".
- Trixie refers to the Fourth Wall as "The Fourth". And quotes Yoda.
- The dragon's cave is atop Bald Mountain.
- The foreshadowing of a dark threat building in the south may be an allusion to Mordor and the War of the Ring in The Lord of the Rings.
- Celestia notes that evil sorcerers like Sombra never seem to stay dead, because there's always one crazed lunatic who'll sacrifice a hoof to bring them back.
- In episode 9, Pinkie accidentally says a line from the My Little Pony fan animation Dusk's Dawn.
- During a conversation about who the worst Abridged Series director is, Celestia, Luna and a royal guard mention Sherclop Pones, Greg Hoffman and Wacarb.
- In episode 10, Fluttershy warns Twilight not to feed the bugs (parasprites) after midnight, a reference to Gremlins. (What makes it even funnier is that Fluttershy is giving the wrong piece of advice; the one thing parasprites and gremlins have in common is their capacity for self-replication, but Fluttershy only gives the instruction that prevents gremlins from becoming evil. The correct advice is "don't let them near water".)
- Applejack refers to the parasprites as "darn tribblets!"—a portmanteau of Tribbles (from Star Trek: The Original Series) and AJ's trademark insult "niblet".
- Pinkie makes several direct references to other MLP abridged series in her song, including Friendship is Witchcraft and My Little Pony: The Mentally Advanced Series.
- The palace guards' reactions are audio samples from "Wombo Combo", a particularly memetic Super Smash Bros. Melee video. (Jack Getschman also made several "Ponified Wombo Combo" videos prior to starting Scootertrix.)
- The "Wombo Combo" audio samples from the last episode continue to haunt Twilight.
- Apple Bloom quotes from Sun Tzu's The Art of War, which is apparently part of the curriculum at the military academy.
- Apple Bloom's "Schlieffenpony Plan" for dealing with the Changeling and Crystal Empires is based on and named after Germany's Schlieffen Plan, their strategy for dealing with enemies on two sides in World War I. Both plans are unsuccessful, too.
- There's one last "Wombo Combo" sample, when Rainbow Dash overtakes Applejack.
- Pinkie quotes Yoda again, once more using the Force/Fourth analogy:Pinkie Pie: Life breathes it. Makes it grow. Its energy surrounds us, and binds us.
- Pinkie tells Twilight "You can't handle the truth", presumably making the reference to the famous courtroom scene in A Few Good Men.
- The airship is named Jabberwocky.
- Scootaloo paraphrases one of the Joker's speeches:Scootaloo: But turning them into stone is too... quick. You can't savor all those little... emotions.
- Apple Bloom calls Scootaloo "Miss Blood and Guts", which may be a reference to General Patton's famous nickname.
- The tune that Sweetie Belle is randomly humming is the theme from Atlantis: The Lost Empire.
- Apple Bloom quips, "No battle plan ever survives contact with the enemy." This is one of many variations on Helmuth von Moltke's far-less-pithy original: "No plan of operations extends with any certainty beyond the first contact with the main hostile force."
- Apple Bloom's raucous "get noscoped!" exclamation is a reference to this Call of Duty internet meme.
- The airship Black Häxan is named after the 1922 movie Häxan.
- The Jessicas are all terrified of The Candymare, villain of the horror fanfic Something Sweet to Bite.
- In episode 20, the changeling pony who mistakenly walks on two legs is Frostbright, the OC of animator Mr KupKake. (According to Getschman and Zimbauer, this wasn't an intentional shout out, but rather a convenient resource that they found online).
- In episode 22, Celestia's line, "You've all done very well!" is a reference to Are You Being Served?.
- Fluttershy has a tube of Cronenberg Lotion. Naturally, it causes gross lumps to break out where it's applies.
"Trixie the Abridged":
- Trixie's calling Twilight fat is almost certainly another reference to Ultra Fast Pony, which had whole seasons' worth of fat jokes at Twilight's expense.
- The fake Related Videos screen includes a thumbnail for a blind commentary video by Rarity Dash- which can be found here—the first Youtube reacter to feature Scootertrix.
- Once again, Pinkie refrences Star Wars: "I felt a great disturbance, a tremor in the Fourth."
- The battle with King Sombra turns into a redubbed version of Fall of the Crystal Empire.
- When Discord mind-controls Pinkie into killing her friends, Pinkie starts reenacting Cupcakes. Then The Bird fails to follow the correct script, so the scene turns into a reenactment of Smile HD instead.
- The Scootertrix and Kanterlot universes are designated "Universe A" and "Universe 1", respectively—the same universe-naming convention used in the Futurama episode "The Farnsworth Parabox". note
- Celestia's plan for trolling Lyra in episode 5 is a reference to the plot of the classic MLP fanfic Anthropology.
- As acknowledged in episode 19, Sombra's battle plan borrows a lot from The Phantom Menace (what with the army that stops functioning if you take out the central controller, and the force field that repels projectiles but doesn't stop an opponent from just walking through).