The standard game design model of Square Enix is to establish the plot, characters and art of the game first. Battle systems, field maps and cutscenes are created next. A typical game of the company involves a team of at most 200 people. Square Enix doesn't usually use other companies' engines, preferring to code from scratch. According to Taku Murata, Square Enix has settled into this game making model since Square's Final Fantasy VII in 1997 and did not try other approaches since, as Enix did not have any internal development studio. Similar to Sony's Greatest Hits program, Square Enix sometimes re-releases games under the Ultimate Hits label, a designation given to games that have achieved a certain level of sales, at a reduced retail price.

Headquarters are located in Shibuya-ku, Tokyo, Japan.