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."

In a 1995 interview with the game's designer Koichi Ishii, found within the Family Computer Magazine and Famitsu, he was asked how the game's team created the "three-dimensional" quality in the game's map, characters and monsters. He responded:

"For example, take a boss battle like the fight with Mispolm. That battle is presented to the player from a certain visual angle. If you completely ignore the background when you’re creating the sprites, then the sense of orientation of the scene gets completely messed up. That’s why we had the sprite artists and the background artists work in tandem for SD3, communicating closely with each other as they went.

We’re aiming for something better than Disney. Also, for shadows and the like, we’re using deep blues and purples instead of shades of black, to impart a sense of softness. If you use black for that there’s a tendency for things to look cold and sterile. As I mentioned, visually we wanted to go for a more storybook, fantasy vibe rather than something realistic. It’s the same direction we went with in Secret of Mana, but in that game we didn’t have enough memory to fully express what we wanted."

The SNES allowed developers to display graphics in layers. If the player character goes to sleep, an emulator can be used to move the blanket sprite covering the lower half of the character's body while they are sleeping to reveal more detailed sleeping sprites that normally cannot be seen, with Angela in particular revealed to be sleeping half-naked.

There were two factors that prevented Seiken Densetsu 3 from being localized back in the mid 1990s. According to former Squaresoft employer Fehdrau, the first was that there were glitches in the Japanese version that wouldn't be able to pass Nintendo of America's certification process. According to Retro Gamer Magazine, the second one was that there was a lot of text. Squaresoft (now Square Enix) declared that fixing these issues for a localization would be too costly on a system that late in its life cycle.

There seems to be a planned boss in the place where the party meets Jagan for the first time in Bucca Island that was removed prior to release that can only be accessed by using Action Replay on sample cartridges of the game. The boss's body is submerged under the water and attacks with two tentacles.