In a 1995 interview with the game's director Hiromichi Tanaka and designer Koichi Ishii, found within the Family Computer Magazine and Famitsu, they were asked when did they began planning out the game. They commented:

Tanaka: "We started drafting the plans for SD3 two years ago. We then went through a period of trial-and-error, where we programmed a lot of different systems, erased them, programmed them anew, erased them… and so forth, until finally we came up with something we now like."

Ishii: "We more or less wanted SD3 to be a continuation of Secret of Mana, but we ended up scrapping all the code from Secret of Mana. It was like, “All these parts that weren’t interesting, let’s try starting from a blank slate and finding another way.” So we essentially reconstructed all the programming for SD3 anew."