In the Japanese version of the game, the Zora Queen's smooth gem is not a source of her power. The gem is actually her secret to beauty, and she turned fat when she lost her gem. Any reference was changed to power in the US version.

One of the Zora in Zora's Domain says he's fond of the Queen being fat, but in the US he just says that they have to get the gem back. After getting the gem back to Oren, that same Zora was disappointed that Oren became slim again. Another Zora mentions the queen's beauty returning, but it was changed to just "What a relief."

After completing the House of Gales, a Zora says that he was swimming with the queen but lost her, even saying that he lost her because she was so slim. In the US version, nothing about weight was mentioned. It seems likely that these changes were made as Nintendo of America didn't want people to think the game was fat shaming people.

During development the energy gauge was green, not purple.

The song used in the Japanese commercials for the game is a remix of an infamous song used in the Japanese A Link to the Past commercials.

Using the sand rod on a Geldman in the desert region will cause it to pop out of the sand wearing red speedos and run away.

During the Nintendo Direct on October 1st 2013, Iwata mentioned that fans saw a physical resemblance between the shop keeper Ravio, and Nabbit from New Super Mario Bros U. Iwata explained that although they are not the same character, since the Mario and Zelda games are developed on the same floor at the Nintendo of Japan Headquarters, the developers may have inspired one another unknowingly.

The jingle the weather vanes make when saving the game is the same tune that is played by the flute/ocarina in The Legend of Zelda: A Link to the Past. In that game, if Link plays it for the weather vane in Kakariko village, it will releasing a duck that can be summoned by playing the flute, and will carry him around Hyrule.

A stylized portrait what appears to be Link's uncle from A Link to the Past hangs in Link's house in A Link Between Worlds.

What appear to be paintings of Medli and Makar's instruments from The Legend of Zelda: The Wind Waker appear in the Milk Bar of A Link Between Worlds.

Portraits of Makar's face and the Crawfish Symbol on Link's shirt from The Legend of Zelda: The Wind Waker appear on the wall of a house in Kakariko Village in A Link Between Worlds.

A thief girl can be found in a cave, and when spoken to will say "How about we keep this a secret to everybody?" This is a reference to the iconic phrase "It's a secret to everybody" found in the original Legend of Zelda.

The Priest ('Shinpu' in Japan which means 'Priest') retains his name in all versions of the game, despite having it previously changed by Nintendo of America to 'The Loyal Sage' in all versions outside of Japan in the original The Legend of Zelda: A Link to the Past, to avoid any religious references.

If you don't buy anything from the Lakeside Item Seller, he will say "... Ay lliw nihtemos yub..." which is "...buy something will yA ..." backwards, a reference to the line said by shopkeepers in the original The Legend of Zelda.

Everything in the game is slanted to achieve the perspective seen in The Legend of Zelda: A Link to the Past.

When the Lorule Castle theme is reversed, part of it resembles the Hyrule Castle theme.

Majora's Mask can be seen on the wall of Ravio's store.