In addition to the cross promotional items and Sega-related items, Phantasy Star Online 2 also has a few other references, a few of which might be a result of Konami being a competitor to Sega.

The Duel Gaze is an obvious reference to a Duel Disk from Yu-Gi-Oh! Unlike other talisman weapons in the game, it is apparently strapped to the wielder's arm and is not held by a handle. It also has an unlockable ability called "Trap Activated"(Wana Hatsudo), which boosts the power of ranger traps, in spite of being an techer weapon (albeit one that is equipable by all classes). The Red Duel Gazer likewise has an unlockable ability called "Trap Master" (Takumi wana-shi).

A reference to Metal Gear Solid can be found in the talisman weapon "Metalisolidom", a weapon that is dropped by Transmizer, an enemy which bears an uncanny resemblance to Metal Gear REX. Other Lilipia mechs are also commonly referred to by western players as Metal Gears, though the fact they are on Lilipia might actually be a reference to Laputa from Myazaki's Castle in The Sky which, like Lilipia, is also based on Gulliver's Travels.

While there was an Attack On Titan collaboration, the fight against Magatsu plays homage to it without directly using any of the Attack on Titan material. Instead of 3D Maneuver Gear, the Phantasy Star Crew utilized the previously introduced jump pads, as well as a buff that boosted jump height partway through the first quest where you fight it. Additionally, the trailer/opening featuring Magatsu similarly appears to be a homage to Attack On Titan.