Various Easter eggs are hidden in the game's character files, most of which require their extensions to be manually altered:

• If the player changes the extension for Monika's character file to .png, the resulting image depicts a square of white noise inside a ring of fire and cracks. Converting the white noise to binary gives a text message encrypted in Base64. Decrypting it reveals what appears to be a monologue from Monika, who mentions a "Third Eye" that causes "some kind of deja vu," which is how she and the other girls are able to perceive alterations to the game's data.
• If the player changes the extension for Natsuki's character file to .jpeg, the resulting image file depicts a painting of a white-haired girl with blank white eyes. The image is heavily distorted, requiring the player to invert its colors and change its rectangular coordinates to polar ones in an image editor in order to view it properly.
• If the player changes the extension for Sayori's character file to .ogg, the resulting audio will become a discordant shriek, similar to that normally heard when converting a data file to audio. However, running sayori.ogg through a spectrograph reveals a QR code which, when scanned, leads to a fictitious examination report for a character named Libitina; her last name and a procedure administered to her are both redacted with a series of X's. Of note is that like Monika's hidden monologue, the report repeatedly mentions a "third eye."
• If the player opens Yuri's character file in a text editor, the result will be a message encrypted in Base64; the file extension does not need to be modified in order to do this. Decrypting the message reveals that it's "I Found a Box Containing the Story of a 19-Year-Old Girl Who Killed a Random Person for No Reason", a creepypasta that was anonymously posted on Thought Catalog in June 2015, over two years before Doki Doki Literature Club's release. In a Twitter reply, developer Dan Salvato confirmed that he was the creepypasta's author and the one who hid it in the game.

If the player deletes Monika's character file before playing a fresh game,Spoiler: Sayori will become aware that she's in a game and begin to panic before deleting all the remaining character files, resulting in an "END" screen with a chromatic image of Sayori's suicide.

During Act 3, if the player is recording through OBS or similar software, Monika will address the audience and then perform a jumpscare.

During Act 3,Spoiler: Monika will make a short reference to the Super Smash Bros. series of games. She says the following sentence. "Hey, have you heard of a game called Super Sma--". She then interrupts herself and continues the conversation.

The credits scene begins with static, which slowly resolves into a scrolling sequences of distorted images. These images appear to be distorted and discolored versions of Monika.

During the first act, Spoiler:Yuri mentions how she has a large collection of intricate knives, however she stabs herself with a large, plain kitchen knife. Dan Salvato, the main developer of the game, later confirmed in a Reddit AMA that this was an artistic error.