Leftover files for Yoshitaka Mine, the antagonist of Yakuza 3, can be found in the files for Yakuza Kiwami, suggesting that he may have been planned to appear in a substory in a similar way to how Yakuza 2's main antagonist, Ryuji Goda, was a substory character in Yakuza 0.

Yakuza 2 features a side story called “The Enka Life” where an NPC sings a song titled "The Moonlight Snows of Kamurocho". In Yakuza 3, this song would go on to be one of the songs Kiryu can sing in the karaoke minigame under the name “Kamurocho Lullaby” and would continue to be used in select future entries.

The character Andre Richardson from Yakuza 3 is notorious for speaking in poor English despite him being American, with one line especially where he says:


In saying the line, "roof" is pronounced more as "ruff". This meme was referenced with his return in Like a Dragon: Infinite Wealth, where in the English dub, after Ichiban spends a night at the bar he runs, he says the line:


And during this line he says the word roof in a similar matter.

Yakuza 3 features an unused remix of a song called “Bruise” in the game files, originally intended to be used in tag battles in the Coliseum. This song would later be used in-game in Like a Dragon Gaiden: The Man Who Erased His Name in 2023.

The texture for Goro Majima’s jacket in Yakuza 3 is of noticeably poorer quality from his appearence in other games. This has even led to a mod being made which replaces his jacket in Yakuza 3 Remastered for PC with a model more close to his jacket in Yakuza 4 Remastered.