There is a hidden questline in the game that is not trackable and only progressed by finding letters, each one a Key Item referred to as "A Family's Escape", hinting to where the next one would be. This questline follows a family that is fleeing the island of Tsushima who are leaving notes for an unaccounted family member named "Toku". Spoiler:The fate of the family and of Toku are left ambiguous by the quest's end.

Toshihiro Nagoshi, the general director of the Yakuza series, was awestruck by Ghosts of Tsushima and its depiction of Japanese culture, history, and aesthetic, even going so far as to say that it was something they (Japanese game developers) should've made. He furthermore said it broke the misconception that western people do not understand Japanese culture.

There is a trophy called "Cooper Clan Cosplayer" that the player can achieve by wearing a specific combination of items. The required items to be worn are:

• The Crooked Kama headband.
• Gosaku's Armor with the Ocean's Guardian dye applied.
• The Sly Tanuki sword kit.

The trophy and items worn are all a reference to Sly Cooper.

A sword kit called the "Sly Tanuki" can be found at the Iwai Village Pillar of Honor. The name and design of the sword kit is a reference to Sly Cooper. The sword kit's description reads: "For the samurai who knows neither friend nor foe... only destruction." is a reference to a quote from Murray, one of Sly's gang members. He tells Sly that he hopes his entrance did not cause him harm, saying, "The Thunder Flop knows neither friend nor foe, only destruction."

Located atop the Jogaku Temple in the Kamiagata region you can find a piece of vanity Gear called the "Crooked Kama Headband". The headband shows the signature weapon of another Sucker Punch Productions character, Sly Cooper.

After completing the game, the player will wake up in Jin's home where a table can be found with a multitude of origami figures referencing several IPs and studios that contributed to Sony's success, including:

• Gran Turismo with a red sports car.
• Horizon Zero Dawn with a Longneck machine.
• Ratchet and Clank with Ratchet's head.
• Days Gone with Deacon's motorcycle.
• Shadow of the Colossus with Gaius the Colossus.
• The Last of Us with a guitar.
• God of War with Kratos' axe.
• Concrete Genie with a paintbrush.
• MLB The Show with a bat and baseball.
• Dreams with an imp wearing glasses.
• PlayStation London Studios with its own logo.
• Kojima Productions also with its own logo.