Normally, when the player decides to build a public works project, Isabelle will prevent the player from going to the beach while scouting out a potential site due to the instability of the sand there. However, if the player uses cheats or glitches to bring Isabelle to the beach and then talks to her, she will give them the option to state whether or not they want to start construction. Despite this, she will deny the request anyway if the player answers yes; however, she will not cite the quality of the ground, but rather will state that there is no available space. Depending on where they are standing, she will state that the proposed site is either too close to the ocean or too close to the cliff, statements which do not otherwise come up in normal gameplay. This dialogue implies that building public works projects on the beach was considered at one point in development.

If a male character is given a feminine piece of clothing, like a dress or skirt, his running animation will also change to be more feminine.

Depending on the number of times the player presses the A button when listening to Resetti for the seventh time, different dialogues will be displayed.

A new day in the game begins at 6am. If the player is playing when this happens, Isabelle will make an announcement telling everyone to get up, and a loading screen will come up. The game will then save, and teleport the player to their house.

On the official UK website, clicking on K.K. Slider in the background will play Totaka's Song.

The monkey villager Champ was originally intended to appear in New Leaf, but was replaced by the new character Flip, who is also a jock and a monkey, for unknown reasons.

Sitting under the Town Tree and waiting for a moment will cause a list of the town's accomplishments, villagers, and other facts will scroll on the screen like credits.

According to an "Iwata Asks" interview, the reduction of Mr. Resetti's duties to an optional event (where they could only see him by developing the Reset Surveillance Center, which only appears as a Public Works Project after resetting the game once) was not only to mirror the Japanese government's budget revisions, but also because Resetti was considered annoying by many players, and made younger ones cry on some occasions. Yet, he still appeared due to the amount of positive attention towards him from the fanbase.

If three holes are dug around the player while near a certain part of the river, the camera will shake violently and allow the player to trip into the river and walk around if they are wearing a King Tut's mask or has bad luck that day. This can be done to allow public works projects to be put into the river or ocean, as well as flowers to be planted there.

At 3:33am on Sundays, and Mondays, a UFO will interrupt the white noise static that is shown on TV, followed by an alien delivering a message. The alien broadcast lasts for a minute before going back to static.

When travelling to the Wi-Fi Tropical Island, Kapp'n will whistle Totaka's song after about 3 minutes if the internet connection is slow.

Hidden in the game is Totaka's Song, a short 19-note melody commonly hidden in the games that the composer Kazumi Totaka has worked on. The song is found in Club LOL and is part of any song that DJ KK is playing.

When you talk to Gulliver he will mention The Overthere, a reference to Chapter 7 in Super Paper Mario.

If you watch TV early in the morning, you may see a short exercise program. This is a real exercise program that is shown every morning in Japan called "Raijio Taisou", or "Radio Exercise".

Whilst speaking with Gulliver, he will at one point state how small your town's port is. He will then talk about another port he visited called Isle Delfino, a place in Super Mario Sunshine.

During early development, Isabelle didn't have a real name, but was instead referred to as simply "Secretary" (ひしょ, Hisho). In the Japanese final release, her name is Shizu (しずえ), likely as a reference to her breed of dog, a Shih Tzu.

The character Gulliver makes a few references to older Nintendo games. One of these references is about the side character Bobbery from Rougeport in Paper Mario: The Thousand Year Door.

During some conversations with Gulliver, after agreeing to help him remember what country he was headed to, he mentions Ricco Harbor, a location from Super Mario Sunshine.

In the game, Kapp'n sometimes talks about cucumbers. This is because Kapp'n is a Kappa from Japanese folklore. Kappas are seen as very mischievous creatures, but if you give them a cucumber, they are said to leave you alone.

When you speak to Gulliver for the first time in the game, he says, "This sure is a fuzzy pickle!" which references EarthBound's photographer.