After the merger with Enix Corporation in April 1st, 2003; Square Europe would become Square Enix Europe.

Not much later in July 2nd, 2004; it was announced that former Atlus USA president and CEO John Yamamoto would be taking over the reins at the European headquarters of the firm, with his new role being as president and CEO. One of the highlighted changes was Square Enix Europe Ltd. would be known simply as Square Enix Ltd, tying in with a new global naming scheme which also saw Square Enix USA becoming Square Enix Inc.

Much later, in February 2009, Square Enix would absorb Eidos Interactive. This would take over known Western IPs such as Deus Ex, Tomb Raider, Thief, and Hitman. After the acquisition it was announced this branch would temptingly be named Square Enix Europe, like the old name of the publishing firm.

In 2022, the assets of Square Enix Europe would be acquired by Embracer Group after the publisher was not satisfied by their sales performance the past years.

Square Enix's European publishing branch still exists to this day as Square Enix Limited.