- Makuta Teridax's mask◊ resembles the helmets worn in the 1997 UFO LEGO sets.
- The walls of the Sanctum in the Mata Nui Online Game include packaging information from a LEGO set and a quote from Douglas Adams's The Hitchhiker's Guide to the Galaxy series: "What do you get if you multiply six by nine?"
- The phrase "play well", LEGO's slogan and meaning of the company's name, is used in Kolhii.
- A line spoken by Matau makes a reference to Julius Caesar's famous sentence "Veni, Vidi, Vici": "We came, we scouted, we all-conquered!"
- A particular quote from the Shadowed One ("I think enough hands have been removed this year") was an allusion by Greg Farshtey to the excessive losses of hands during lightsaber combat in Star Wars Episode III: Revenge of the Sith, which was also released in 2005.
- The second Mask of Life code for Command Toa Matoro is former BZPower administrator and former BIONICLE.com Webmaster, Kelly (AKA Binkmeister's) initials. This was done as a thanks to all the work he had done to the site.
- Antroz's poem about killing the Toa was based off the famous children's rhyme "Ten Little Indians".
- Vultraz's joke about clicking his red feet together in Brother In Arms is a reference to the classic movie The Wizard of Oz.
- Several characters are named after LEGO staffers:
- Jerbraz's name is based off Jeremy Brazeal, who was an artist for BIONICLE: World and the young readers BIONICLE: Journey of Takanuva, BIONICLE: The Secret of Certavus, and BIONICLE: Desert of Danger.
- Tobduk's name is based off of Toby Dutkiewicz's name, one of the artists for BIONICLE: World.
- Johmak's name is based off that of John McCormack, an artist for BIONICLE: World.
- Tren Krom was inspired by H.P. Lovecraft's character Cthulhu. BIONICLE writer Greg Farshtey stated this to be a "tip of the hat" to the author.
- Antidermis being a green liquid that's said to be the essence of evil itself is a reference to the John Carpenter film, Prince of Darkness; where green liquid is the essence of Satan.
- Vezon's comment about his one-hundred ten unanswered questions in Destiny War is a reference to the large number of storyline questions Greg Farshtey receives via the personal messaging system on BZPower, some of which inevitably go unanswered.
- Greg Farshtey is an avid World of Warcraft player. Even names such as the Great Cataclysm and The Shattering are lifted directly from there.
- Federation of Fear has a shout-out to Jaws:
- Vezon: We're gonna need...Brutaka: A bigger boat, I know.
- The Vahki Animations, especially Nuurakh, reference Metropolis. The drone-like workers, the pistons, and manual tedium all draw imagery from the film.
- In the Mata Nui Online Game, Turaga Vakama keeps the idol from the Tintin story The Broken Ear in his hut.
- Brutaka's team of expendable villains, the Federation of Fear, is similar in concept to Suicide Squad.
- The scene in Bionicle 2: Legends of Metru Nui has Turaga Lhikan's blinking heartlight prior to his death, a reference to the Ultra Warriors of Ultra Series with their Color Timers.
Shout Out / BIONICLE