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:

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.

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 unused sprite of Mr. Everdred as a ghost is present in the game's ROM. It is assumed that either he was going to be a party member at one point during development (when one of the party members faints, they will appear as a ghost) or Spoiler:when Mr. Everdred was beaten near Jackie's Cafe in Fourside, a ghost would have flown out of his body. Its true purpose has never been confirmed.

In Mother 2 (the Japanese version of EarthBound), the cultists of Happy Happyism appear with the letters HH on their forehead (for Happy Happyism). In EarthBound, a pom pom was added and the HH was removed, presumably to try to make the cultists look less like members of the Klu Klux Klan. Also, possibly because HH on an already Klan-like sprite could be construed to mean "Heil Hitler". The city "Threek" was renamed "Threed" in EarthBound. Like the cultists, this may also be to avoid any link to the Klan, as Threek could be seen as Three K's, or KKK.

There is a section where Ness will enter his own subconscious. In this segment, the North American version of the game has Ness wearing his Pajamas, but in the Japanese version, Ness is more or less naked, wearing nothing but his hat.

EarthBound's Official Strategy Guide contains pictures of real locations. This may be to give the guide a more realistic feel, as if it wasn't a guide. The strategy guide also includes newspaper articles, which mainly revolve around Ness and his party's journey.

In an Interview with Shigeru Miyamoto about Mother 2 (known as EarthBound in America), he admitted that Mother 2 was the first RPG he beat:

In EarthBound, all the Mr. Saturns talk using a very odd-looking font. They speak using a very strange font in Japanese, too. The Japanese Mr. Saturn font was created by Shigesato Itoi himself. In an interview around the time of MOTHER 1+2's release, he mentions that he based the font on his daughter's handwriting at the time.

During a livestream of the game with EarthBound Central, Marcus Lindblot revealed a couple secrets of the game's localization. For example, the character of Nico from Magicant was based on Marcus' real-life daughter, who was born while he was working on the game. Nobody had known where the name Nico came from prior to this, as the character didn't have that name in the Japanese version.

EarthBound features five types of anti-piracy:

• First, it will simply check to make sure the cartridge isn't being used in a PAL console.
• Second, it will perform two SRAM checks at startup.
• Third, if the first two measures are disabled, the enemies on screen will be ramped up to ridiculous levels and you will find enemies in areas they don't belong in.
• Fourth, there's another SRAM checker that is called up six times during the game. Its purpose is unknown as of yet.
• Fifth and finally, if the game detects problems after Pokey turns off the Devil's Machine, the game will erase all of your save data and freeze, forcing you to go back to reset and find all of your work gone.

In the official strategy guide for EarthBound, there are pages about the town's attractions, accompanied by fun facts, such as:
• Onett Has a population of 3,500 people and 2 dogs.
• Twoson has 10 vendors in the park and 15 mushrooms.
• In Threed, there are 2 Graveyards, 2,000 zombies, and a grand total of 0 lions, tigers, and bears.
• In Dusty Dunes Desert, there are 2,000,001 Cacti, and 5 people living there.
• There is an average of 0 Temper Tantrums in Dalaam.
• Deep Darkness has 4,000,603 Mosquitos.

The "Casey Bat" is the reward for beating Master Puke. This bat is a reference to the old poem "Casey at the Bat" and, as can be expected based on the poem, is very strong but almost never successfully hits enemies.

At the time of EarthBound's development, Shigesato Itoi didn't know how to use computers. He would actually speak each line of dialogue out loud, often one letter at a time, and Matchan Miura typed it up. Itoi used Miura's reactions as a gauge of how good a line was.

The official strategy guide included with all copies of the game contains several errors. For example, it claims that the Kraken enemies in the Sea of Eden drop the Gutsy Bat item. The item is actually found in the Cave of the Past area, dropped by the Bionic Kraken enemy.

The main antagonist of EarthBound, an alien known as "Giygas", was made by Shigesato Itoi and described as "a living being that deserves love." While the character first debuted with a different design as the final boss of Mother, Giygas' appearance in EarthBound was inspired by a childhood incident where Itoi accidentally walked into the wrong movie at a theatre and watched the 1957 Japanese horror film "Kenpei to Barabara Shibijin". Itoi was traumatized by the film, where he confused a lovemaking scene that ends in murder as a rape scene. He says it had a "sense of terror having atrocity and eroticism side-by-side, and that's what Giygas's lines at the end are":

Giygas' weakest form has an outline of a Fetus hidden in it.

In the issue of Weekly Famitsu published in 9th of September 1994, Itoi refers to the battle backgrounds as a "Video Relaxant." The Video Relaxant was going to be an in-game item and was originally referred to as a "Video Drug". It can still be found in the game's files. It has no function and the description of the item is "What the hey is this?"

In the September 1994 issue of Weekly Famitsu, Shigesato Itoi stated that the rolling health meter in battle was originally going to be made of Pachinko beads. The idea came to him when a Pachinko parlor opened right by their office. He thought that the idea would be scary to see a stream of beads rattling out from Ness and his friends. However, it was difficult for them to portray it on screen, as when the amount increased, it covered up 1/3 of the screen.

Shigesato Itoi personally wrote every line of the script in Mother 2 (besides Moonside) to give the characters more personality.