If the player enters Threed's circus tent and repeatedly uses the Check command on the rightmost corner, the game will glitch in a variety of unpredictable ways. The most minor of these outcomes involves a short delay in when the "No problem here." text box is thrown up, while more major results can escalate into full-scale corruptions; most results involve the text box spewing garbage data. The reason for these phenomena is because of a programming oversight: the game stores every map in a single file that players are transported around via warps. However, the corner where the glitch occurs contains a gap in the room's boundaries, enabling the player to use the Check command on out-of-bounds areas that the game was not programmed to read.

Following its discovery, the bug, popularly known as the "Threed Tent Glitch" and the "Check Area Glitch," became a key asset for speedrunners, as one possible effect gives players access to a debug menu, from which they can warp directly to the game's epilogue. Its utility only further increased after players discovered that it can be triggered very early in the game by using additional glitches to reach the top-right corner in Onett's map, which similarly gives access to an out-of-bounds area.

An infamous scratch and sniff ad for EarthBound, featured in magazines around the time of the game's release, caused WayForward director/designer James Montagna to suffer from a severe allergic reaction as a child, which had him rushed to hospital:

The music that plays in Onett's Arcade contains brief snippets of the main theme of Xevious, and of the bonus theme from Nintendo's 1979 arcade game Sheriff.

In a 1997 interview with the game's composer Keiichi Suzuki published in the GSLA, he stated that him and his team did an about-face in their approach to composing the soundtrack, from attempting to create vocal-oriented pop music like in Mother, to concentrate on making solid instrumentals:

As revealed in development files uncovered by the Video Game History Foundation, the woman in Summers who sells Magic Cakes was originally intended to be a masseuse whose oil massages could induce relaxing dreams. This would've more readily explained why Ness and company's first use of her services results in the odd transition into Poo's training in Dalaam, in which the screen turns pinkish-purple and distorts before fading to black.

If you have a full inventory up until the point where Porky's mom squashes Buzz Buzz, he will notice that Ness can't hold the Sound Stone right now and won't give it to him. Instead, he will transport it to Tracy, meaning that you don't have to hold the Sound Stone in your inventory for the entire game and it will still record the melodies of the "Your Sanctuary" locations even in Tracy's possession. Normally, the Sound Stone remains in your inventory for the whole game and cannot be held by Escargo Express. If you do wish to have the Sound Stone back from Tracy, you must talk to her in-person.

By plugging in a second controller and pressing Select during the cutscene where Ness, Porky and Picky encounter the Meteorite and Buzz Buzz, the direction and length of the light that shines from it can be changed. The height in which the cutscene is activated seems to affect how the light behaves, and it seems to be intrinsically linked to where Buzz Buzz's sprite moves on-screen as the light will sometimes follow his looping animation by extending or retracting slightly.

The director for the United States localization needed a name for Porky's father so he named him "Aloysius," a reference to Looney Tunes where Daffy Duck gives the name to a giant to save himself from being giant food, because he thought the name was "dumb and funny."

At the 3rd "Your Sanctuary" location, Milky Well, if there is either a dead or diamondized party member, there will be a typo saying "The power of Milkey Well flowed into [Party Member's Name]."

Some fans have theorized that Jeff's father, Dr. Andonuts, is actually Loid from the original Mother grown up. This can be evidenced by thier similar hair color, glasses, and the fact that they both hide in garbage cans when frightened. It's also important to note that both Loid and Jeff can use bottle rockets as weapons during battle.

The fetch and progress system in the Monkey Cave is similar to that of the "Beneath the Well" mini-dungeon from The Legend of Zelda: Majora's Mask. It's possible that Nintendo was referencing this system in Majora's Mask.

Paula's Theme is a remix of the theme of Youngtown from the original Mother.

Unused miniature sprites of what appear to be the Photo-Man and an Escargo Express delivery man can be found within the game's code, suggesting that they may have appeared in the Lost Underground at some point during development.

Storing a damaged Teddy Bear with the Escargo Express or Tracy after it is damaged, and then checking it out again will restore it to full health.

The last scene of the game's opening cinematic features Ness approaching Giant Step, alone, at nighttime. However, this is impossible to do in the actual game. The only two times that Spoiler:Onett (the town where Giant Step is located) can be explored at night time are at the meteor crash, the search for Picky at the very beginning of the game, and Spoiler:Giygas's last-minute invasion of Onett near the end of the game. During the former, Spoiler:Ness cannot obtain the key to the Shack, which is required to access Giant Step. During the latter, Spoiler:Ness has a full party of four, meaning that he cannot access Giant Step on his own.

Using the Pencil eraser on Ness's Nightmare outside of battle, a dialogue box will say, "Do you really think this look likes a pencil?". Using the Eraser eraser says, "It looks like some sort of primitive human statue if you look at it from the right angle... But it definitely doesn't look like an eraser... does it?"

If there is second controller connected, it's possible to control the game with both controllers.

There are two arcade cabinets found only in the Onett Arcade, which show recognizable screens of the Donkey Kong and Space Invaders arcade games.

The four major cities in EagleLand are all named after numbers: Onett, Twoson, Threed and Fourside.

If the player talks to the trumpet player in Onett, he will play "Symphony No.9 Movement 2" composed by Antonin Dvorak.